Obtain and Plot L1000 Signatures
L1000_signature_data <- read.table(file = "matPH3_2_1_0.2_0.3_L1000_Batch2017_Regina_removed.txt", row.names = 1, header = TRUE)
head(L1000_signature_data) AARS ABCB6 ABCC5 ABCF1 ABCF3 ABHD4 ABHD6 ABL1 ACAA1 ACAT2 ACBD3 ACD ACLY ACOT9 ADAM10 ADAT1 ADCK3 ADH5 ADI1 ADO ADRB2 AGL AKAP8 AKAP8L AKR7A2
10-DEBC 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 0
AKT1 ALAS1 ALDH7A1 ALDOA ALDOC AMDHD2 ANKRD10 ANO10 ANXA7 APBB2 APOE APP APPBP2 ARFIP2 ARHGAP1 ARHGEF12 ARHGEF2 ARID4B ARID5B ARL4C ARNT2
10-DEBC -3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0
ARPP19 ASAH1 ASCC3 ATF1 ATF5 ATF6 ATG3 ATMIN ATP11B ATP1B1 ATP2C1 ATP5S ATP6V0B ATP6V1D AURKA AURKB AXIN1 BACE2 BAD BAG3 BAMBI BAX BCL2 BCL7B
10-DEBC 0 0 0 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 0 0 0 0 -3 0
BDH1 BECN1 BHLHE40 BID BIRC2 BIRC5 BLCAP BLMH BLVRA BMP4 BNIP3 BNIP3L BPHL BRCA1 BTK BUB1B BZW2 C2CD2 C2CD2L C5 CAB39 CALM3 CALU CAMSAP2
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
CANT1 CAPN1 CASC3 CASK CASP10 CASP2 CASP3 CASP7 CAST CAT CBLB CBR1 CBR3 CCDC85B CCDC86 CCDC92 CCL2 CCNA1 CCNA2 CCNB1 CCNB2 CCND1 CCND3 CCNE2
10-DEBC 0 0 -3 -3 0 0 0 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 0 0
CCNF CCNH CCP110 CD320 CD40 CD44 CD58 CDC20 CDC25A CDC25B CDC42 CDC45 CDCA4 CDH3 CDK1 CDK19 CDK2 CDK4 CDK5R1 CDK6 CDK7 CDKN1A CDKN1B CDKN2A
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 4 0 0 0 0 0 0 0
CEBPA CEBPD CEBPZ CENPE CEP57 CERK CETN3 CFLAR CGRRF1 CHAC1 CHEK1 CHEK2 CHERP CHIC2 CHMP4A CHMP6 CHN1 CIAPIN1 CIRBP CISD1 CLIC4 CLPX CLSTN1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 0 0 0
CLTB CLTC CNDP2 CNOT4 CNPY3 COASY COG2 COG4 COG7 COL1A1 COL4A1 COPB2 COPS7A CORO1A CPNE3 CPSF4 CREB1 CREG1 CRELD2 CRK CRKL CRTAP CRYZ CSK
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0
CSNK1A1 CSNK1E CSNK2A2 CSRP1 CTNNAL1 CTNND1 CTSD CTTN CXCL2 CXCR4 CYB561 CYCS CYTH1 DAG1 DAXX DCK DCTD DCUN1D4 DDB2 DDIT4 DDR1 DDX10 DDX42
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0
DECR1 DENND2D DERA DFFA DFFB DHDDS DHRS7 DHX29 DLD DMTF1 DNAJA3 DNAJB1 DNAJB2 DNAJB6 DNAJC15 DNM1 DNM1L DNMT1 DNMT3A DNTTIP2 DPH2 DRAP1 DSG2
10-DEBC 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 3 -3 0 0 0 0 0 -3 0
DUSP11 DUSP14 DUSP22 DUSP3 DUSP4 DUSP6 DYNLT3 DYRK3 E2F2 EAPP EBNA1BP2 EBP ECD ECH1 EDEM1 EDN1 EED EGF EGFR EGR1 EIF4EBP1 EIF4G1 EIF5 ELAC2
10-DEBC 3 0 0 0 0 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 0 0 0 -3
ELAVL1 ELOVL6 EML3 ENOPH1 ENOSF1 EPB41L2 EPHA3 EPHB2 EPN2 EPRS ERBB2 ERBB3 ETFB ETS1 ETV1 EVL EXOSC4 EXT1 EZH2 FAH FAIM FAM20B FAM57A FAM63A
10-DEBC 0 0 -3 0 0 -3 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 3 0 0 0
FAM69A FAS FASTKD5 FAT1 FBXL12 FBXO11 FBXO21 FBXO7 FCHO1 FDFT1 FEZ2 FGFR2 FGFR4 FHL2 FIS1 FKBP14 FKBP4 FOS FOSL1 FOXJ3 FOXO3 FOXO4 FPGS FRS2
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 0 0 0
FSD1 FUT1 FYN FZD1 FZD7 G3BP1 GAA GABPB1 GADD45A GADD45B GALE GAPDH GATA2 GATA3 GDPD5 GFOD1 GFPT1 GHR GLI2 GLOD4 GLRX GMNN GNA11 GNA15 GNAI1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 0
GNAI2 GNAS GNB5 GNPDA1 GOLT1B GPATCH8 GPC1 GRB10 GRB7 GRN GRWD1 GSTM2 GSTZ1 GTF2A2 GTF2E2 GTPBP8 H2AFV HADH HAT1 HDAC2 HDAC6 HDGFRP3 HEATR1
10-DEBC 0 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HEBP1 HERC6 HERPUD1 HES1 HIF1A HIST1H2BK HIST2H2BE HK1 HMG20B HMGA2 HMGCR HMGCS1 HMOX1 HN1L HOMER2 HOOK2 HOXA10 HOXA5 HPRT1 HS2ST1 HSD17B10
10-DEBC 0 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 0 0 0 3 0
HSD17B11 HSPA1A HSPA4 HSPA8 HSPB1 HSPD1 HTATSF1 HTRA1 HYOU1 IARS2 ICAM1 ICAM3 ICMT ID2 IDE IER3 IFNAR1 IFRD2 IGF1R IGF2BP2 IGF2R IGFBP3
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0
IGHMBP2 IKBKAP IKBKB IKBKE IKZF1 IL13RA1 IL1B IL4R ILK INPP1 INPP4B INSIG1 INTS3 IPO13 IQGAP1 ISOC1 ITFG1 ITGAE ITGB1BP1 ITGB5 JMJD6 JUN
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
KAT6A KAT6B KCNK1 KCTD5 KDELR2 KDM3A KDM5A KDM5B KEAP1 KIAA0100 KIAA0196 KIAA0355 KIAA0753 KIAA0907 KIAA1033 KIF14 KIF20A KIF2C KIF5C KIT
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 -4 0 0 -3 0 0 3
KLHDC2 KLHL21 KLHL9 KTN1 LAGE3 LAMA3 LAP3 LBR LGALS8 LGMN LIG1 LIPA LOXL1 LPAR2 LPGAT1 LRP10 LRPAP1 LRRC16A LRRC41 LSM5 LSM6 LSR LYN LYPLA1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 0 0 0 3 0 0 3
LYRM1 MACF1 MALT1 MAMLD1 MAN2B1 MAP2K5 MAP3K4 MAP4K4 MAP7 MAPK13 MAPK1IP1L MAPK9 MAPKAPK2 MAPKAPK3 MAPKAPK5 MAST2 MAT2A MBNL1 MBNL2 MBOAT7
10-DEBC 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 0 0 0 0 0 0
MBTPS1 MCM3 MCOLN1 ME2 MEF2C MELK MEST METRN MFSD10 MICALL1 MIF MKNK1 MLEC MLLT11 MMP1 MMP2 MNAT1 MOK MPZL1 MRPL12 MRPL19 MRPS16 MRPS2 MSH6
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MSRA MTA1 MTF2 MTFR1 MTHFD2 MUC1 MVP MYBL2 MYC MYCBP MYCBP2 MYL9 MYLK MYO10 NARFL NCAPD2 NCK1 NCK2 NCOA3 NENF NET1 NFATC3 NFATC4 NFE2L2 NFIL3
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 0 0 0 0
NFKB2 NFKBIA NFKBIB NFKBIE NGRN NIPSNAP1 NISCH NIT1 NMT1 NNT NOL3 NOLC1 NOS3 NOSIP NOTCH1 NPC1 NPDC1 NPEPL1 NPRL2 NR1H2 NR2F6 NR3C1 NRAS
10-DEBC 0 0 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
NRIP1 NSDHL NT5DC2 NUCB2 NUDCD3 NUDT9 NUP133 NUP62 NUP85 NUP88 NUP93 NUSAP1 NVL ORC1 OXA1L OXCT1 OXSR1 P4HA2 P4HTM PACSIN3 PAF1 PAFAH1B1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
PAFAH1B3 PAICS PAK1 PAK4 PAK6 PAN2 PAPD7 PARP1 PARP2 PAX8 PCBD1 PCCB PCK2 PCM1 PCMT1 PCNA PDGFA PDHX PDIA5 PDLIM1 PDS5A PECR PEX11A PFKL
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 0 0 0 0 0
PGAM1 PGM1 PGRMC1 PHGDH PHKA1 PHKB PHKG2 PIGB PIH1D1 PIK3C2B PIK3C3 PIK3CA PIK3R3 PIK3R4 PIN1 PIP4K2B PKIG PLA2G15 PLA2G4A PLCB3 PLEKHJ1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
PLEKHM1 PLK1 PLOD3 PLP2 PLS1 PLSCR1 PLSCR3 PMAIP1 PMM2 PNKP PNP POLB POLD4 POLE2 POLG2 POLR1C POLR2I POLR2K POP4 PPARD PPARG PPIC PPIE PPOX
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 3 0 0 0 3 0 0
PPP1R13B PPP2R3C PPP2R5A PPP2R5E PRAF2 PRCP PRKACA PRKAG2 PRKCD PRKCH PRKCQ PRKX PROS1 PRPF4 PRR15L PRR7 PRSS23 PRUNE PSIP1 PSMB10 PSMB8
10-DEBC 0 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 0 0 0 0 0
PSMD10 PSMD2 PSMD4 PSMD9 PSME1 PSME2 PSMF1 PSMG1 PSRC1 PTGS2 PTK2 PTK2B PTPN1 PTPN12 PTPN6 PTPRC PTPRF PTPRK PUF60 PWP1 PXMP2 PXN PYCR1 PYGL
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0
RAB11FIP2 RAB21 RAB27A RAB31 RAB4A RAC2 RAD51C RAD9A RAE1 RAI14 RALA RALB RALGDS RAP1GAP RASA1 RB1 RBKS RBM15B RBM34 RBM6 REEP5 RELB RFC2
10-DEBC -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 0 -5 0 0 0
RFC5 RFNG RFX5 RGS2 RHEB RHOA RNF167 RNH1 RNMT RNPS1 RPA1 RPA2 RPA3 RPIA RPL39L RPN1 RPP38 RPS5 RPS6 RPS6KA1 RRAGA RRP12 RRP1B RRP8 RRS1 RSU1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
RTN2 RUVBL1 S100A13 S100A4 SACM1L SATB1 SCAND1 SCARB1 SCCPDH SCP2 SCRN1 SCYL3 SDHB SENP6 SERPINE1 SESN1 SFN SGCB SH3BP5 SHB SHC1 SIRT3 SKIV2L
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3
SKP1 SLC11A2 SLC1A4 SLC25A13 SLC25A14 SLC25A4 SLC25A46 SLC27A3 SLC2A6 SLC35A1 SLC35A3 SLC35B1 SLC35F2 SLC37A4 SLC5A6 SMAD3 SMARCA4 SMARCC1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0
SMARCD2 SMC1A SMC3 SMC4 SMNDC1 SNAP25 SNCA SNX11 SNX13 SNX6 SNX7 SOCS2 SORBS3 SOX2 SOX4 SPAG4 SPAG7 SPDEF SPEN SPP1 SPR SPRED2 SPTAN1 SPTLC2
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -4 0 0 0 0 0
SQRDL SQSTM1 SRC SSBP2 ST3GAL5 ST6GALNAC2 ST7 STAMBP STAP2 STAT1 STAT3 STAT5B STK10 STK25 STMN1 STUB1 STX1A STX4 STXBP1 STXBP2 SUPV3L1
10-DEBC 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 0 0 0
SUV39H1 SUZ12 SYK SYNE2 SYNGR3 SYPL1 TARBP1 TATDN2 TBC1D9B TBP TBPL1 TBX2 TBXA2R TCEA2 TCEAL4 TCERG1 TCFL5 TCTA TCTN1 TERF2IP TERT TES TESK1
10-DEBC 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0
TEX10 TFAP2A TFDP1 TGFB3 TGFBR2 THAP11 TIAM1 TICAM1 TIMELESS TIMM17B TIMM22 TIMM9 TIMP2 TIPARP TJP1 TLE1 TLK2 TLR4 TM9SF2 TM9SF3 TMCO1 TMED10
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TMEM109 TMEM110 TMEM2 TMEM5 TMEM50A TMEM97 TNFRSF21 TNIP1 TOMM34 TOMM70A TOP2A TOPBP1 TOR1A TP53 TP53BP1 TP53BP2 TPD52L2 TPM1 TRAK2 TRAM2
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TRAP1 TRAPPC3 TRAPPC6A TRIB1 TRIB3 TRIM13 TRIM2 TSC22D3 TSEN2 TSKU TSPAN3 TSPAN4 TSPAN6 TSTA3 TUBB6 TWF2 TXLNA TXNDC9 TXNL4B TXNRD1 UBE2A
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 -4 0
UBE2C UBE2J1 UBE2L6 UBE3B UBE3C UBQLN2 UBR7 UFM1 UGDH USP1 USP14 USP22 USP6NL USP7 UTP14A VAPB VAT1 VAV3 VDAC1 VGLL4 VPS28 VPS72 WASF3 WDR61
10-DEBC 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0
WDR7 WDTC1 WFS1 WIPF2 WRB XBP1 XPNPEP1 XPO7 YKT6 YME1L1 YTHDF1 ZDHHC6 ZFP36 ZMIZ1 ZMYM2 ZNF131 ZNF274 ZNF318 ZNF395 ZNF451 ZNF586 ZNF589 ZW10
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[ reached 'max' / getOption("max.print") -- omitted 5 rows ]target_compound <- "triptolide"
compound_sig <- as.data.frame(t(subset(L1000_signature_data, rownames(L1000_signature_data) == target_compound)))
compound_sig <- subset(compound_sig, compound_sig$triptolide != 0)
data <- compound_sig$triptolide
names(data) <- rownames(compound_sig)
data ABCF1 ABCF3 ABHD6 ABL1 ACAA1 ACBD3 ACD ACLY ACOT9 ADAM10 ADAT1 ADCK3 ADH5
7 -6 7 -4 4 -7 5 -6 -7 -5 7 -3 -3
ADI1 ADO AGL AKAP8 AKAP8L ALAS1 ALDH7A1 ALDOC AMDHD2 ANO10 ANXA7 APBB2 APOE
3 -7 5 -6 7 6 7 5 4 5 -5 6 6
APPBP2 ARFIP2 ARHGAP1 ARHGEF12 ARHGEF2 ARID4B ARID5B ARL4C ARNT2 ARPP19 ASAH1 ASCC3 ATF1
3 -6 4 -5 -7 -3 3 5 7 -5 3 -5 -7
ATF5 ATG3 ATMIN ATP11B ATP1B1 ATP2C1 ATP5S ATP6V0B AURKA AURKB BACE2 BAD BAG3
-3 -7 -5 7 -7 3 -5 4 -7 6 6 4 -6
BAMBI BAX BCL2 BCL7B BHLHE40 BID BIRC2 BLCAP BLMH BLVRA BMP4 BNIP3 BNIP3L
5 6 6 -7 -5 6 -6 -3 -4 -5 6 -4 -6
BPHL BRCA1 BTK BUB1B C2CD2 C2CD2L C5 CAB39 CALM3 CALU CAMSAP2 CANT1 CASC3
4 -7 6 7 3 7 7 -6 7 3 6 -5 -5
CASK CASP10 CASP2 CASP3 CASP7 CAST CAT CBLB CBR1 CBR3 CCDC92 CCL2 CCNA1
-5 7 -5 4 -6 7 6 6 3 -3 3 3 5
CCNA2 CCNB1 CCNB2 CCND3 CCNF CCNH CCP110 CD320 CD40 CD44 CDC20 CDC25A CDC25B
-7 -6 -7 3 -7 3 -6 5 7 7 -7 -7 -6
CDC42 CDC45 CDCA4 CDH3 CDK1 CDK19 CDK4 CDK5R1 CDK7 CDKN1B CDKN2A CEBPD CEBPZ
-6 7 -7 5 -5 -4 -6 5 -7 -6 3 7 -5
CENPE CERK CGRRF1 CHAC1 CHEK1 CHEK2 CHERP CHIC2 CHMP6 CHN1 CLIC4 CLPX CLTB
-3 7 -6 7 -4 -7 -5 -3 6 4 -6 -7 6
CLTC CNDP2 CNOT4 CNPY3 COG4 COG7 COL1A1 COPB2 COPS7A CORO1A CPNE3 CPSF4 CREG1
-7 -4 -7 5 7 7 4 -3 6 4 -4 6 3
CRELD2 CRK CRKL CRTAP CRYZ CSK CSNK1A1 CSNK1E CSNK2A2 CSRP1 CTNND1 CTSD CXCR4
7 -3 5 3 -4 -4 -4 6 7 -4 7 7 5
CYCS CYTH1 DAXX DCK DCUN1D4 DDB2 DDR1 DDX10 DDX42 DECR1 DFFA DFFB DHDDS
5 4 7 -7 3 -6 6 -7 -7 6 7 6 7
DHRS7 DHX29 DLD DMTF1 DNAJA3 DNAJB1 DNAJB6 DNM1 DNMT1 DNTTIP2 DPH2 DUSP11 DUSP14
-3 -4 -3 4 6 -7 6 4 6 -3 -3 7 -3
DYRK3 E2F2 EAPP EBNA1BP2 EBP ECD ECH1 EDEM1 EDN1 EED EGF EGFR EIF4G1
7 7 -6 -4 -4 -5 6 5 7 -6 6 -6 4
EIF5 ELAC2 ELOVL6 EML3 ENOPH1 EPHA3 EPHB2 EPN2 EPRS ERBB2 ETS1 EVL EXT1
-5 3 -5 7 -7 3 5 6 -6 -7 7 4 7
EZH2 FAH FAIM FAM20B FAM57A FAM63A FAM69A FAS FASTKD5 FBXL12 FBXO11 FBXO21 FBXO7
-6 7 5 4 -5 5 6 -3 -6 6 -5 3 -5
FCHO1 FDFT1 FEZ2 FGFR2 FGFR4 FHL2 FKBP14 FKBP4 FOS FOSL1 FOXJ3 FOXO3 FOXO4
6 -4 -3 7 7 -6 3 6 7 -3 -5 -4 -3
FRS2 FSD1 FUT1 FZD1 FZD7 G3BP1 GAA GABPB1 GADD45A GADD45B GALE GAPDH GDPD5
7 7 7 7 -6 -5 4 -7 7 3 -7 -3 7
GFOD1 GLI2 GLOD4 GLRX GMNN GNA11 GNA15 GNAS GNB5 GOLT1B GPATCH8 GPC1 GRB7
7 6 -7 -7 6 -4 7 -4 7 -4 -7 7 7
GRN GRWD1 GSTM2 GSTZ1 GTF2A2 GTF2E2 GTPBP8 H2AFV HAT1 HDAC2 HEATR1 HERC6 HIF1A
5 -6 5 3 -4 -7 -6 7 3 -7 -6 4 -5
HIST1H2BK HIST2H2BE HK1 HMGCR HMGCS1 HMOX1 HN1L HOMER2 HOOK2 HOXA10 HOXA5 HS2ST1 HSPA1A
3 7 -5 5 -7 -5 -4 6 3 -5 -3 5 -5
HSPA4 HSPA8 HSPD1 HTATSF1 HTRA1 HYOU1 IARS2 ICAM1 ICAM3 ID2 IDE IER3 IFNAR1
7 -7 -3 7 7 5 -5 6 -5 -3 -3 -4 7
IFRD2 IGF1R IGF2BP2 IGF2R IGFBP3 IGHMBP2 IKBKAP IKBKB IKBKE IKZF1 IL13RA1 IL1B IL4R
-3 -4 -4 7 6 5 -6 7 6 7 7 6 7
INPP1 INPP4B INSIG1 INTS3 IPO13 IQGAP1 ISOC1 ITFG1 ITGAE ITGB5 JMJD6 JUN KAT6A
-5 -5 -3 -6 7 7 5 7 5 3 -6 5 -4
KCNK1 KCTD5 KDM3A KDM5A KDM5B KIAA0196 KIAA0355 KIAA0753 KIAA0907 KIAA1033 KIF14 KIF20A KIF2C
-4 6 -7 -6 3 6 4 6 -3 -7 -6 -7 -6
KIF5C KIT LAGE3 LAP3 LBR LGALS8 LGMN LOXL1 LPAR2 LPGAT1 LRPAP1 LSM5 LSM6
-6 7 3 6 -7 7 7 3 4 -6 6 -3 -5
LSR LYN LYPLA1 MACF1 MAN2B1 MAP2K5 MAP3K4 MAP4K4 MAPK1IP1L MAPK9 MAPKAPK2 MAPKAPK3 MAPKAPK5
7 6 -5 -7 7 5 -7 -5 -7 6 -3 3 -4
MAT2A MBNL1 MBNL2 MBTPS1 MCM3 MCOLN1 MELK MEST MICALL1 MKNK1 MMP1 MMP2 MNAT1
-7 -7 -7 6 -7 7 -4 7 -7 6 6 6 -6
MPZL1 MRPL12 MRPL19 MRPS16 MRPS2 MSH6 MSRA MTA1 MTF2 MTFR1 MTHFD2 MVP MYBL2
-6 -7 -3 -6 -7 -7 5 3 -7 6 -7 7 7
MYC MYCBP2 MYL9 MYO10 NARFL NCAPD2 NCK1 NCK2 NCOA3 NENF NET1 NFATC4 NFE2L2
-5 4 6 -4 7 4 -7 -5 4 5 -4 7 6
NFKB2 NFKBIA NFKBIB NFKBIE NGRN NISCH NIT1 NOL3 NOLC1 NOS3 NOTCH1 NPC1 NPDC1
4 -7 6 7 7 4 7 6 -5 5 7 -4 6
NPEPL1 NPRL2 NR1H2 NR2F6 NRIP1 NSDHL NT5DC2 NUCB2 NUDCD3 NUDT9 NUP62 NUP85 NUP88
5 5 5 -4 -7 -4 6 4 -3 -6 -7 -7 -6
NUSAP1 NVL ORC1 OXA1L OXCT1 OXSR1 P4HTM PAF1 PAFAH1B1 PAICS PAPD7 PARP2 PAX8
-6 7 7 -5 5 -6 6 7 7 -5 6 -7 5
PCCB PCK2 PCM1 PCMT1 PCNA PDGFA PDHX PDLIM1 PDS5A PECR PFKL PGM1 PHKA1
3 6 -7 -6 -7 -7 -6 4 -5 6 5 -3 5
PHKB PHKG2 PIH1D1 PIK3C2B PIK3CA PIK3R3 PIK3R4 PIP4K2B PLA2G4A PLCB3 PLEKHM1 PLK1 PLOD3
7 6 6 -4 6 3 -5 -6 7 5 7 -7 5
PLP2 PLS1 PMAIP1 PMM2 PNP POLD4 POLE2 POLG2 POLR1C POLR2K POP4 PPARD PPOX
7 3 7 6 -4 -4 -7 -4 3 -4 -7 7 7
PPP1R13B PPP2R3C PPP2R5E PRCP PRKACA PRKCQ PRKX PROS1 PRPF4 PRR15L PRR7 PRSS23 PRUNE
7 -6 4 6 6 7 7 3 -6 7 6 -3 -3
PSIP1 PSMB10 PSMB8 PSMD10 PSMD2 PSMD4 PSMD9 PSMF1 PSMG1 PSRC1 PTGS2 PTK2 PTK2B
-5 4 -3 -6 6 -4 4 7 -7 -4 5 -5 7
PTPN1 PTPN12 PTPRC PTPRF PTPRK PUF60 PWP1 PXN RAB21 RAB27A RAB31 RAB4A RAC2
5 -6 7 7 6 -7 -7 7 7 4 5 -5 4
RAD51C RAD9A RAE1 RAI14 RALA RALB RAP1GAP RASA1 RBKS RBM15B RBM34 RBM6 RFNG
4 -5 -7 7 3 -6 4 -3 3 5 -5 3 6
RFX5 RGS2 RHEB RNH1 RNMT RNPS1 RPA2 RPA3 RPL39L RPP38 RPS5 RPS6 RRAGA
-5 -4 -7 7 -7 -6 5 -5 -3 -7 3 -5 -4
RRP12 RRP1B RRP8 RSU1 RTN2 RUVBL1 SACM1L SCAND1 SCARB1 SCCPDH SCP2 SCYL3 SDHB
6 -7 -3 4 7 6 -6 -6 7 -4 5 -6 -3
SENP6 SERPINE1 SFN SGCB SHB SHC1 SIRT3 SLC11A2 SLC25A13 SLC25A46 SLC27A3 SLC2A6 SLC35A3
-7 6 -3 3 6 4 5 5 -5 -6 6 -3 -3
SLC35B1 SLC35F2 SLC37A4 SLC5A6 SMAD3 SMARCA4 SMARCC1 SMC3 SMC4 SMNDC1 SNAP25 SNCA SNX11
-4 -7 -6 3 -6 -5 -5 -4 -7 -5 6 5 -7
SNX13 SNX7 SOCS2 SOX2 SOX4 SPAG4 SPAG7 SPDEF SPEN SPR SPRED2 SPTAN1 SPTLC2
6 7 7 7 -5 4 7 3 -6 -4 7 -3 -6
SQRDL SQSTM1 SRC SSBP2 ST3GAL5 ST6GALNAC2 ST7 STAMBP STAP2 STAT5B STK10 STUB1 STX4
4 -6 -3 6 5 3 -7 -7 7 5 7 -3 7
STXBP1 STXBP2 SUPV3L1 SUV39H1 SUZ12 SYK SYNE2 SYPL1 TARBP1 TATDN2 TBP TBPL1 TBX2
-5 5 7 -7 -7 5 -4 -3 6 -6 -7 -4 4
TBXA2R TCEA2 TCERG1 TCTA TCTN1 TERF2IP TERT TES TESK1 TFAP2A TGFB3 TGFBR2 THAP11
6 7 -7 3 5 -5 7 4 7 7 7 -6 -4
TICAM1 TIMELESS TIMM17B TIMM22 TIMM9 TIMP2 TIPARP TJP1 TLE1 TLR4 TM9SF2 TMED10 TMEM110
3 3 -4 7 -7 7 3 -4 -6 -4 -6 4 7
TMEM2 TMEM5 TMEM50A TMEM97 TOMM70A TOP2A TOR1A TP53BP1 TP53BP2 TPD52L2 TPM1 TRAK2 TRAM2
-5 -5 -3 -7 -7 -7 5 -4 4 6 -4 -7 -4
TRAP1 TRAPPC3 TRAPPC6A TRIB3 TRIM13 TRIM2 TSEN2 TSKU TUBB6 TWF2 TXLNA TXNDC9 TXNRD1
7 -7 7 4 7 5 -3 -5 -3 -5 -7 -4 -6
UBE2C UBE2J1 UBE2L6 UBE3B UBR7 USP1 USP14 USP22 USP6NL USP7 VAT1 VAV3 VDAC1
-7 7 6 7 -3 -6 3 -7 -6 -7 -3 6 -4
VGLL4 VPS28 VPS72 WASF3 WDR61 WDR7 WIPF2 WRB XBP1 XPNPEP1 XPO7 YKT6 YTHDF1
-5 -6 4 4 -6 7 -4 -4 -6 -3 -6 -7 -6
ZDHHC6 ZFP36 ZMYM2 ZNF131 ZNF395 ZNF589 ZW10
-4 3 -6 -7 7 6 -4 barplot(data, horiz = TRUE, col = "red")
pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)
pdf(file = "triptolide_sig_heatmap.pdf")
pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)
dev.off()pdf
3
So now subset this signature for genes within different medulloblastoma disease signatures. A good way to pick which one is ideal is to find which one this drug reverses the disease signature most of.
So let’s load in the medulloblastoma disease signature data from Anna. - This is a microarray dataset, so some genes have multiple probes. These probes are labeled for specificity, but for this purpose we will just average duplicate rows, so each gene’s reported fold-change is representative of all probes for each gene.
First, we should subset columns that are averagable.. ie. numeric So Fold-change.
Then we will avverage the fold changes within each gene, and use that to calculate signature overlap with compound response signatures.
library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, unionMedulloSigs <- read.csv(file = "MedulloSigs.csv", skip = 1, header = TRUE)
head(MedulloSigs) X G4 G4.1 G4.2 G4.3 G4.4 G4.5 G4.6 G4.7 G4.8 G4.9 G4.10 G4.11 G4.12 G4.13 G4.14
1 1007_s_at 7.595940 7.806655 7.401414 7.603100 7.996856 7.825205 7.683266 7.457205 7.562213 7.349231 7.692980 6.847049 6.988782 7.347686 7.491087
2 1053_at 6.144400 6.191544 5.907811 6.052795 6.883360 6.283014 5.882486 6.577583 5.841223 6.801283 6.385026 6.321308 6.137943 6.116995 6.906354
3 117_at 4.824306 5.244389 4.805659 4.051785 4.535820 4.763028 4.822698 3.484312 4.938065 4.363099 5.048573 4.287716 4.467057 3.517498 4.783316
4 121_at 5.670915 5.621487 5.978379 5.599533 5.769882 5.278115 5.732694 5.846439 5.827768 5.992464 5.660527 5.930387 5.950121 5.687315 6.205769
5 1255_g_at 4.141546 3.417727 4.218036 3.653252 3.535145 3.683867 3.781914 3.970292 3.443618 3.384390 3.718438 4.067316 3.975936 5.742682 6.078101
6 1294_at 5.489351 5.704782 5.436774 5.157905 5.551020 5.652489 5.562603 4.999911 5.572154 5.659134 5.755425 5.354698 5.767070 5.429784 5.430661
G4.15 G4.16 G4.17 G4.18 G4.19 G4.20 G4.21 G4.22 G4.23 G4.24 G4.25 G4.26 G4.27 G4.28 G4.29 G4.30
1 7.481837 7.670195 7.220520 7.658086 7.767983 6.940416 7.127614 6.386037 7.178317 7.387895 7.024382 7.156177 7.432957 6.742055 7.073693 7.285918
2 6.583686 6.274951 6.270232 6.959778 6.529857 6.283947 6.006599 6.608406 5.874931 6.296741 6.148041 6.606785 5.929855 6.291013 7.048820 6.531606
3 4.784153 4.865224 3.811097 4.720283 5.874088 4.608166 4.804021 4.255613 5.142832 5.258536 4.741448 4.440296 3.605498 3.600048 3.916015 4.422449
4 5.967428 5.742362 5.824524 5.388158 6.076265 6.026107 5.838604 5.771130 5.280153 5.179534 5.875493 5.623295 5.231109 5.210578 5.786283 5.412539
5 4.560173 4.671894 3.377588 4.782479 4.383276 4.953712 4.062166 5.261653 4.169761 7.480992 4.993150 4.371976 3.214868 5.308268 4.345103 4.618086
6 5.176150 5.137562 5.019925 5.267858 5.007965 5.054333 5.605802 5.013963 5.152135 5.991465 5.282188 4.852030 5.077047 5.295313 5.063860 5.064492
G4.31 G4.32 G4.33 G4.34 G4.35 G4.36 G4.37 G4.38 G3 G3.1 G3.2 G3.3 G3.4 G3.5 G3.6 G3.7
1 6.946303 7.805026 7.751303 7.649788 7.330798 7.500640 7.667673 7.757735 7.792349 8.260027 7.332892 7.128977 6.899421 6.170656 7.302496 7.727711
2 6.224955 6.617671 6.372637 6.606785 5.766757 6.388730 6.606110 6.893149 6.579529 7.080868 6.642747 6.012002 6.596873 6.690097 6.358189 6.204356
3 4.999911 4.498698 3.317816 3.613617 4.067316 4.136765 4.429626 3.756538 4.907495 5.773620 6.098074 4.794964 4.833898 5.285232 4.154184 4.415220
4 5.220356 5.660875 5.980151 5.861640 5.938591 5.984188 5.436774 6.090857 6.212406 6.282827 6.110358 5.918625 6.018593 5.894954 5.746522 6.061457
5 3.462606 4.652054 5.874650 4.259859 3.912023 4.172848 4.930871 3.676301 3.152736 3.404525 4.483003 6.736730 4.616110 3.616309 5.146913 6.079933
6 4.762174 4.976734 5.428029 5.705115 5.177279 4.112512 5.232178 5.925859 5.472691 6.110802 5.416989 4.933034 5.138149 5.334167 4.807294 4.941642
G3.8 G3.9 G3.10 G3.11 G3.12 G3.13 G3.14 G3.15 WNT WNT.1 WNT.2 WNT.3 WNT.4 WNT.5 WNT.6 WNT.7
1 7.287560 6.780603 7.560757 6.719979 7.536524 6.942350 7.408894 6.756235 7.600802 7.725507 6.760878 7.165107 6.799502 7.647977 6.919091 6.641443
2 6.734591 6.830982 6.795929 7.313420 6.337003 6.025624 6.564560 6.335409 5.974064 6.624198 6.735305 6.163946 6.448573 6.202940 6.602316 6.553648
3 5.101694 4.949469 5.183467 4.417635 3.508556 4.530447 5.073297 3.992681 5.362700 4.853591 4.325456 5.057519 3.610918 4.461300 4.130355 4.306764
4 5.905362 5.780435 5.378514 5.666773 5.862210 5.369708 5.897429 5.580861 5.785977 5.922650 5.800607 5.441985 5.772686 5.318610 5.808143 5.411200
5 6.037632 5.415656 5.078294 3.921973 6.176075 4.332048 5.868732 5.468060 3.328627 3.779634 3.214868 4.301359 3.713572 3.218876 3.716008 5.013963
6 5.252274 4.420045 4.989071 5.109575 4.703204 5.046646 5.066385 5.382199 6.133398 4.886583 5.068904 4.864453 5.165357 5.551796 4.950177 4.668145
SHH SHH.1 SHH.2 SHH.3 SHH.4 SHH.5 SHH.6 SHH.7 SHH.8 SHH.9 MEDIAN_OVERALL MEDIAN_G4 MEDIAN_G3 MEDIAN_WNT MEDIAN_SHH
1 7.545496 7.937874 7.673595 6.877605 6.945340 7.776745 7.462502 7.460433 7.466914 7.750744 7.432957 7.457205 7.295028 7.042099 7.506205
2 6.178773 6.507725 6.100991 6.377067 6.315358 6.776963 6.173369 6.482343 6.058188 6.541607 6.377067 6.296741 6.588201 6.501111 6.346213
3 5.790877 4.588024 4.453184 4.797442 4.725616 4.714921 4.445002 5.213848 4.563306 4.163559 4.588024 4.498698 4.870697 4.393378 4.651472
4 6.218002 5.592478 5.796361 6.023205 5.615680 5.797880 5.792709 5.859931 5.993961 6.115450 5.797880 5.771130 5.896191 5.779331 5.828906
5 4.614130 4.025352 3.962716 3.487375 3.246491 4.584968 4.338597 3.532226 4.599152 4.044804 4.218036 4.172848 5.112603 3.714790 4.035078
6 5.677096 5.467638 5.564137 5.925325 5.566434 5.626901 5.357529 5.349961 5.822750 5.554121 5.282188 5.282188 5.087980 5.009540 5.565285
Log2FC_G4 Log2FC_G3 Log2FC_WNT Log2FC_SHH X.1 Probe.Set.ID Gene.Symbol X.2 X.3 X.4 X.5 X.6 X.7
1 0.004698740 -0.02702275 -0.077930753 0.014147430 NA 1007_s_at DDR1 TRUE NA NA NA NA NA
2 -0.018287712 0.04699153 0.027793137 -0.006997209 NA 1053_at RFC2 TRUE NA NA NA NA NA
3 -0.028365417 0.08625515 -0.062542306 0.019814559 NA 117_at HSPA6 TRUE NA NA NA NA NA
4 -0.006671645 0.02425791 -0.004622849 0.007699538 NA 121_at PAX8 TRUE NA NA NA NA NA
5 -0.015539038 0.27748674 -0.183290752 -0.063974847 NA 1255_g_at GUCA1A TRUE NA NA NA NA NA
6 0.000000000 -0.05404265 -0.076457372 0.075320050 NA 1294_at UBA7 TRUE NA NA NA NA NAmyvars <- c("Gene.Symbol", "Log2FC_G4", "Log2FC_G3", "Log2FC_WNT", "Log2FC_SHH")
dat <- MedulloSigs[myvars]
myvars2 <- c("Log2FC_G4", "Log2FC_G3", "Log2FC_WNT", "Log2FC_SHH")
dat2 <- dat %>% group_by(Gene.Symbol) %>% mutate_each(funs(mean), -(0)) %>% distinctfuns() is soft deprecated as of dplyr 0.8.0
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
[90mThis warning is displayed once per session.[39mhead(dat2)rownames(dat2) <- dat2$Gene.SymbolSetting row names on a tibble is deprecated.MedulloSigs <- dat2
rm(dat)
rm(dat2)Now, let’s subset this medullo data for the genes that are in the compound response signature. Then, we can assess differential discordance.
head(MedulloSigs)head(compound_sig) triptolide
ABCF1 7
ABCF3 -6
ABHD6 7
ABL1 -4
ACAA1 4
ACBD3 -7cmpdGenes <- rownames(compound_sig)
# obj.transpose <- t(obj@assays$SCT@scale.data)
cmpd_overlap <- rownames(MedulloSigs)[which(rownames(MedulloSigs) %in% cmpdGenes)]
overlap <- MedulloSigs[cmpd_overlap,] # FileA
overlap rownames(overlap) <- overlap$Gene.SymbolSetting row names on a tibble is deprecated.
# overlap$Gene.Symbol <- NULL
head(overlap)
cmpd_ordered <- as.numeric(as.vector(t(compound_sig)))
names(cmpd_ordered) <- rownames(compound_sig)
cmpd_ordered ABCF1 ABCF3 ABHD6 ABL1 ACAA1 ACBD3 ACD ACLY ACOT9 ADAM10 ADAT1 ADCK3 ADH5
7 -6 7 -4 4 -7 5 -6 -7 -5 7 -3 -3
ADI1 ADO AGL AKAP8 AKAP8L ALAS1 ALDH7A1 ALDOC AMDHD2 ANO10 ANXA7 APBB2 APOE
3 -7 5 -6 7 6 7 5 4 5 -5 6 6
APPBP2 ARFIP2 ARHGAP1 ARHGEF12 ARHGEF2 ARID4B ARID5B ARL4C ARNT2 ARPP19 ASAH1 ASCC3 ATF1
3 -6 4 -5 -7 -3 3 5 7 -5 3 -5 -7
ATF5 ATG3 ATMIN ATP11B ATP1B1 ATP2C1 ATP5S ATP6V0B AURKA AURKB BACE2 BAD BAG3
-3 -7 -5 7 -7 3 -5 4 -7 6 6 4 -6
BAMBI BAX BCL2 BCL7B BHLHE40 BID BIRC2 BLCAP BLMH BLVRA BMP4 BNIP3 BNIP3L
5 6 6 -7 -5 6 -6 -3 -4 -5 6 -4 -6
BPHL BRCA1 BTK BUB1B C2CD2 C2CD2L C5 CAB39 CALM3 CALU CAMSAP2 CANT1 CASC3
4 -7 6 7 3 7 7 -6 7 3 6 -5 -5
CASK CASP10 CASP2 CASP3 CASP7 CAST CAT CBLB CBR1 CBR3 CCDC92 CCL2 CCNA1
-5 7 -5 4 -6 7 6 6 3 -3 3 3 5
CCNA2 CCNB1 CCNB2 CCND3 CCNF CCNH CCP110 CD320 CD40 CD44 CDC20 CDC25A CDC25B
-7 -6 -7 3 -7 3 -6 5 7 7 -7 -7 -6
CDC42 CDC45 CDCA4 CDH3 CDK1 CDK19 CDK4 CDK5R1 CDK7 CDKN1B CDKN2A CEBPD CEBPZ
-6 7 -7 5 -5 -4 -6 5 -7 -6 3 7 -5
CENPE CERK CGRRF1 CHAC1 CHEK1 CHEK2 CHERP CHIC2 CHMP6 CHN1 CLIC4 CLPX CLTB
-3 7 -6 7 -4 -7 -5 -3 6 4 -6 -7 6
CLTC CNDP2 CNOT4 CNPY3 COG4 COG7 COL1A1 COPB2 COPS7A CORO1A CPNE3 CPSF4 CREG1
-7 -4 -7 5 7 7 4 -3 6 4 -4 6 3
CRELD2 CRK CRKL CRTAP CRYZ CSK CSNK1A1 CSNK1E CSNK2A2 CSRP1 CTNND1 CTSD CXCR4
7 -3 5 3 -4 -4 -4 6 7 -4 7 7 5
CYCS CYTH1 DAXX DCK DCUN1D4 DDB2 DDR1 DDX10 DDX42 DECR1 DFFA DFFB DHDDS
5 4 7 -7 3 -6 6 -7 -7 6 7 6 7
DHRS7 DHX29 DLD DMTF1 DNAJA3 DNAJB1 DNAJB6 DNM1 DNMT1 DNTTIP2 DPH2 DUSP11 DUSP14
-3 -4 -3 4 6 -7 6 4 6 -3 -3 7 -3
DYRK3 E2F2 EAPP EBNA1BP2 EBP ECD ECH1 EDEM1 EDN1 EED EGF EGFR EIF4G1
7 7 -6 -4 -4 -5 6 5 7 -6 6 -6 4
EIF5 ELAC2 ELOVL6 EML3 ENOPH1 EPHA3 EPHB2 EPN2 EPRS ERBB2 ETS1 EVL EXT1
-5 3 -5 7 -7 3 5 6 -6 -7 7 4 7
EZH2 FAH FAIM FAM20B FAM57A FAM63A FAM69A FAS FASTKD5 FBXL12 FBXO11 FBXO21 FBXO7
-6 7 5 4 -5 5 6 -3 -6 6 -5 3 -5
FCHO1 FDFT1 FEZ2 FGFR2 FGFR4 FHL2 FKBP14 FKBP4 FOS FOSL1 FOXJ3 FOXO3 FOXO4
6 -4 -3 7 7 -6 3 6 7 -3 -5 -4 -3
FRS2 FSD1 FUT1 FZD1 FZD7 G3BP1 GAA GABPB1 GADD45A GADD45B GALE GAPDH GDPD5
7 7 7 7 -6 -5 4 -7 7 3 -7 -3 7
GFOD1 GLI2 GLOD4 GLRX GMNN GNA11 GNA15 GNAS GNB5 GOLT1B GPATCH8 GPC1 GRB7
7 6 -7 -7 6 -4 7 -4 7 -4 -7 7 7
GRN GRWD1 GSTM2 GSTZ1 GTF2A2 GTF2E2 GTPBP8 H2AFV HAT1 HDAC2 HEATR1 HERC6 HIF1A
5 -6 5 3 -4 -7 -6 7 3 -7 -6 4 -5
HIST1H2BK HIST2H2BE HK1 HMGCR HMGCS1 HMOX1 HN1L HOMER2 HOOK2 HOXA10 HOXA5 HS2ST1 HSPA1A
3 7 -5 5 -7 -5 -4 6 3 -5 -3 5 -5
HSPA4 HSPA8 HSPD1 HTATSF1 HTRA1 HYOU1 IARS2 ICAM1 ICAM3 ID2 IDE IER3 IFNAR1
7 -7 -3 7 7 5 -5 6 -5 -3 -3 -4 7
IFRD2 IGF1R IGF2BP2 IGF2R IGFBP3 IGHMBP2 IKBKAP IKBKB IKBKE IKZF1 IL13RA1 IL1B IL4R
-3 -4 -4 7 6 5 -6 7 6 7 7 6 7
INPP1 INPP4B INSIG1 INTS3 IPO13 IQGAP1 ISOC1 ITFG1 ITGAE ITGB5 JMJD6 JUN KAT6A
-5 -5 -3 -6 7 7 5 7 5 3 -6 5 -4
KCNK1 KCTD5 KDM3A KDM5A KDM5B KIAA0196 KIAA0355 KIAA0753 KIAA0907 KIAA1033 KIF14 KIF20A KIF2C
-4 6 -7 -6 3 6 4 6 -3 -7 -6 -7 -6
KIF5C KIT LAGE3 LAP3 LBR LGALS8 LGMN LOXL1 LPAR2 LPGAT1 LRPAP1 LSM5 LSM6
-6 7 3 6 -7 7 7 3 4 -6 6 -3 -5
LSR LYN LYPLA1 MACF1 MAN2B1 MAP2K5 MAP3K4 MAP4K4 MAPK1IP1L MAPK9 MAPKAPK2 MAPKAPK3 MAPKAPK5
7 6 -5 -7 7 5 -7 -5 -7 6 -3 3 -4
MAT2A MBNL1 MBNL2 MBTPS1 MCM3 MCOLN1 MELK MEST MICALL1 MKNK1 MMP1 MMP2 MNAT1
-7 -7 -7 6 -7 7 -4 7 -7 6 6 6 -6
MPZL1 MRPL12 MRPL19 MRPS16 MRPS2 MSH6 MSRA MTA1 MTF2 MTFR1 MTHFD2 MVP MYBL2
-6 -7 -3 -6 -7 -7 5 3 -7 6 -7 7 7
MYC MYCBP2 MYL9 MYO10 NARFL NCAPD2 NCK1 NCK2 NCOA3 NENF NET1 NFATC4 NFE2L2
-5 4 6 -4 7 4 -7 -5 4 5 -4 7 6
NFKB2 NFKBIA NFKBIB NFKBIE NGRN NISCH NIT1 NOL3 NOLC1 NOS3 NOTCH1 NPC1 NPDC1
4 -7 6 7 7 4 7 6 -5 5 7 -4 6
NPEPL1 NPRL2 NR1H2 NR2F6 NRIP1 NSDHL NT5DC2 NUCB2 NUDCD3 NUDT9 NUP62 NUP85 NUP88
5 5 5 -4 -7 -4 6 4 -3 -6 -7 -7 -6
NUSAP1 NVL ORC1 OXA1L OXCT1 OXSR1 P4HTM PAF1 PAFAH1B1 PAICS PAPD7 PARP2 PAX8
-6 7 7 -5 5 -6 6 7 7 -5 6 -7 5
PCCB PCK2 PCM1 PCMT1 PCNA PDGFA PDHX PDLIM1 PDS5A PECR PFKL PGM1 PHKA1
3 6 -7 -6 -7 -7 -6 4 -5 6 5 -3 5
PHKB PHKG2 PIH1D1 PIK3C2B PIK3CA PIK3R3 PIK3R4 PIP4K2B PLA2G4A PLCB3 PLEKHM1 PLK1 PLOD3
7 6 6 -4 6 3 -5 -6 7 5 7 -7 5
PLP2 PLS1 PMAIP1 PMM2 PNP POLD4 POLE2 POLG2 POLR1C POLR2K POP4 PPARD PPOX
7 3 7 6 -4 -4 -7 -4 3 -4 -7 7 7
PPP1R13B PPP2R3C PPP2R5E PRCP PRKACA PRKCQ PRKX PROS1 PRPF4 PRR15L PRR7 PRSS23 PRUNE
7 -6 4 6 6 7 7 3 -6 7 6 -3 -3
PSIP1 PSMB10 PSMB8 PSMD10 PSMD2 PSMD4 PSMD9 PSMF1 PSMG1 PSRC1 PTGS2 PTK2 PTK2B
-5 4 -3 -6 6 -4 4 7 -7 -4 5 -5 7
PTPN1 PTPN12 PTPRC PTPRF PTPRK PUF60 PWP1 PXN RAB21 RAB27A RAB31 RAB4A RAC2
5 -6 7 7 6 -7 -7 7 7 4 5 -5 4
RAD51C RAD9A RAE1 RAI14 RALA RALB RAP1GAP RASA1 RBKS RBM15B RBM34 RBM6 RFNG
4 -5 -7 7 3 -6 4 -3 3 5 -5 3 6
RFX5 RGS2 RHEB RNH1 RNMT RNPS1 RPA2 RPA3 RPL39L RPP38 RPS5 RPS6 RRAGA
-5 -4 -7 7 -7 -6 5 -5 -3 -7 3 -5 -4
RRP12 RRP1B RRP8 RSU1 RTN2 RUVBL1 SACM1L SCAND1 SCARB1 SCCPDH SCP2 SCYL3 SDHB
6 -7 -3 4 7 6 -6 -6 7 -4 5 -6 -3
SENP6 SERPINE1 SFN SGCB SHB SHC1 SIRT3 SLC11A2 SLC25A13 SLC25A46 SLC27A3 SLC2A6 SLC35A3
-7 6 -3 3 6 4 5 5 -5 -6 6 -3 -3
SLC35B1 SLC35F2 SLC37A4 SLC5A6 SMAD3 SMARCA4 SMARCC1 SMC3 SMC4 SMNDC1 SNAP25 SNCA SNX11
-4 -7 -6 3 -6 -5 -5 -4 -7 -5 6 5 -7
SNX13 SNX7 SOCS2 SOX2 SOX4 SPAG4 SPAG7 SPDEF SPEN SPR SPRED2 SPTAN1 SPTLC2
6 7 7 7 -5 4 7 3 -6 -4 7 -3 -6
SQRDL SQSTM1 SRC SSBP2 ST3GAL5 ST6GALNAC2 ST7 STAMBP STAP2 STAT5B STK10 STUB1 STX4
4 -6 -3 6 5 3 -7 -7 7 5 7 -3 7
STXBP1 STXBP2 SUPV3L1 SUV39H1 SUZ12 SYK SYNE2 SYPL1 TARBP1 TATDN2 TBP TBPL1 TBX2
-5 5 7 -7 -7 5 -4 -3 6 -6 -7 -4 4
TBXA2R TCEA2 TCERG1 TCTA TCTN1 TERF2IP TERT TES TESK1 TFAP2A TGFB3 TGFBR2 THAP11
6 7 -7 3 5 -5 7 4 7 7 7 -6 -4
TICAM1 TIMELESS TIMM17B TIMM22 TIMM9 TIMP2 TIPARP TJP1 TLE1 TLR4 TM9SF2 TMED10 TMEM110
3 3 -4 7 -7 7 3 -4 -6 -4 -6 4 7
TMEM2 TMEM5 TMEM50A TMEM97 TOMM70A TOP2A TOR1A TP53BP1 TP53BP2 TPD52L2 TPM1 TRAK2 TRAM2
-5 -5 -3 -7 -7 -7 5 -4 4 6 -4 -7 -4
TRAP1 TRAPPC3 TRAPPC6A TRIB3 TRIM13 TRIM2 TSEN2 TSKU TUBB6 TWF2 TXLNA TXNDC9 TXNRD1
7 -7 7 4 7 5 -3 -5 -3 -5 -7 -4 -6
UBE2C UBE2J1 UBE2L6 UBE3B UBR7 USP1 USP14 USP22 USP6NL USP7 VAT1 VAV3 VDAC1
-7 7 6 7 -3 -6 3 -7 -6 -7 -3 6 -4
VGLL4 VPS28 VPS72 WASF3 WDR61 WDR7 WIPF2 WRB XBP1 XPNPEP1 XPO7 YKT6 YTHDF1
-5 -6 4 4 -6 7 -4 -4 -6 -3 -6 -7 -6
ZDHHC6 ZFP36 ZMYM2 ZNF131 ZNF395 ZNF589 ZW10
-4 3 -6 -7 7 6 -4 cmpd_ordered2 <- cmpd_ordered[cmpd_overlap] # Character list in brackets orders to fit that character list...
cmpd_ordered2 DDR1 PAX8 SCARB1 PTPRC JMJD6 TLR4 CNPY3 PIP4K2B SNX13 MBNL2 MYO10 TXNDC9 DNAJA3
6 5 7 7 -6 -4 5 -6 6 -7 -4 -4 6
ATP5S CANT1 GNB5 TRAM2 FBXO7 CRTAP GFOD1 ATP11B PSMD10 ARHGEF2 TOR1A PSIP1 FGFR4
-5 -5 7 -4 -5 3 7 7 -6 -7 5 -5 7
PTGS2 LPGAT1 STAT5B TERT ETS1 ASAH1 RNH1 TGFB3 MBNL1 CDC25A RHEB TRIB3 CSNK1A1
5 -6 5 7 7 3 7 7 -7 -7 -7 4 -4
SPEN HOMER2 ITFG1 TSEN2 HEATR1 PHKG2 FAM69A COL1A1 SNAP25 RBM6 TCTN1 BLCAP NT5DC2
-6 6 7 -3 -6 6 6 4 6 3 5 -3 6
SMC3 KIF5C G3BP1 MYCBP2 ZNF131 SHB PCCB GALE CD44 CTNND1 ARID5B SRC ATF1
-4 -6 -5 4 -7 6 3 -7 7 7 3 -3 -7
SYNE2 TPM1 SSBP2 MAP4K4 NOL3 RRP8 RRP12 KAT6A PTK2 ARHGEF12 TIMM17B DDX42 FKBP4
-4 -4 6 -5 6 -3 6 -4 -5 -5 -4 -7 6
MKNK1 DYRK3 RSU1 TXNRD1 TXLNA CCND3 NCOA3 CNDP2 DDX10 HERC6 INPP4B CAST EDN1
6 7 4 -6 -7 3 4 -4 -7 4 -5 7 7
EGFR TATDN2 PRSS23 IKZF1 SUZ12 KCNK1 MMP2 NFE2L2 SOX4 CHERP SERPINE1 IGF2R SMARCA4
-6 -6 -3 7 -7 -4 6 6 -5 -5 6 7 -5
TP53BP1 TRIM13 PRCP CCP110 PPP2R3C STXBP2 BAD RPS5 ABCF1 SPAG7 RNPS1 SMNDC1 ATP6V0B
-4 7 6 -6 -6 5 4 3 7 7 -6 -5 4
RPS6 USP22 CLTC CSRP1 PTPRF DNAJB1 XBP1 GRN HK1 CALU CTSD MAT2A GNAS
-5 -7 -7 -4 7 -7 -6 5 -5 3 7 -7 -4
ECH1 IQGAP1 HSPA1A HSPD1 PAFAH1B1 HYOU1 PSMD2 EPRS PSMD4 TMED10 HIF1A PAICS PSMF1
6 7 -5 -3 7 5 6 -6 -4 4 -5 -5 7
MYL9 SMARCC1 TM9SF2 PXN COPB2 PFKL ITGB5 ACLY PLP2 BHLHE40 TERF2IP HTRA1 LRPAP1
6 -5 -6 7 -3 5 3 -6 7 -5 -5 7 6
CREG1 PCNA LGMN ATP1B1 SYPL1 NUDCD3 TOP2A EBNA1BP2 SCP2 ANXA7 TPD52L2 TRAP1 CAT
3 -7 7 -7 -3 -3 -7 -4 5 -5 6 7 6
MAPKAPK2 JUN SHC1 SQSTM1 USP7 NFKBIA TOMM70A ZFP36 KDM5B MCM3 RAE1 CLIC4 ID2
-3 5 4 -6 -7 -7 -7 3 3 -7 -7 -6 -3
NISCH PWP1 RUVBL1 MBTPS1 INSIG1 RRAGA IER3 UBE2L6 SMC4 USP14 PNP DNMT1 MYBL2
4 -7 6 6 -3 -4 -4 6 -7 3 -4 6 7
RPA2 MTHFD2 DAXX ELAC2 NCAPD2 LBR SCCPDH NET1 HDAC2 BNIP3 CDC25B ATMIN MPZL1
5 -7 7 3 4 -7 -4 -4 -7 -4 -6 -5 -6
IL13RA1 PSRC1 PGM1 KIAA0196 EXT1 PTPN12 TWF2 TJP1 MEST ALDOC ACAA1 KDM5A RAI14
7 -4 -3 6 7 -6 -5 -4 7 5 4 -6 7
BIRC2 PAF1 RALB ARFIP2 ARHGAP1 CPNE3 ABL1 TRAK2 NUP62 PCM1 BLMH MVP PLOD3
-6 7 -6 -6 4 -4 -4 -7 -7 -7 -4 7 5
ARL4C KIAA0907 CRK PLK1 CDK4 MTA1 STXBP1 VPS72 FEZ2 SENP6 ACBD3 CSK CSNK1E
5 -3 -3 -7 -6 3 -5 4 -3 -7 -7 -4 6
TRIM2 RGS2 ABCF3 TCERG1 USP1 MYC SLC35B1 DECR1 PAPD7 H2AFV IKBKAP BCL7B HMGCR
5 -4 -6 -7 -6 -5 -4 6 6 7 -6 -7 5
NRIP1 HTATSF1 ADAM10 EAPP LYN APPBP2 POLR2K ICAM1 PSMB10 SDHB RASA1 GTF2A2 NPC1
-7 7 -5 -6 6 3 -4 6 4 -3 -3 -4 -4
GTF2E2 RNMT RBM15B OXSR1 DUSP11 CCNB2 HIST2H2BE PTPN1 TES EBP PHKB PIK3R3 WRB
-7 -7 5 -6 7 -7 7 5 4 -4 7 3 -4
GPC1 CASP3 DNTTIP2 ZMYM2 OXCT1 MAPKAPK3 INPP1 SACM1L PRKACA INTS3 STAMBP GAA TARBP1
7 4 -3 -6 5 3 -5 -6 6 -6 -7 4 6
SLC37A4 PCK2 FAH POP4 CDC20 CYTH1 NIT1 NUP88 LSM5 MSH6 FAM20B FHL2 CRYZ
-6 6 7 -7 -7 4 7 -6 -3 -7 4 -6 -4
UBE2C RFX5 ARNT2 POLD4 LYPLA1 ECD PTPRK TIMELESS STK10 TCTA PDHX PTK2B TP53BP2
-7 -5 7 -4 -5 -5 6 3 7 3 -6 7 4
SLC11A2 SPTLC2 TBP HAT1 TIMP2 PMM2 MTFR1 CDK1 ST3GAL5 MAPK9 TLE1 IL4R NPRL2
5 -6 -7 3 7 6 6 -5 5 6 -6 7 5
FBXO11 CDH3 DFFA EDEM1 HS2ST1 KIAA0355 CNOT4 DMTF1 DCK BAMBI NCK2 IDE PPP2R5E
-5 5 7 5 5 4 -7 4 -7 5 -5 -3 4
CEBPZ MTF2 EZH2 DUSP14 SOCS2 APOE PSMG1 DDB2 CCNA2 EML3 SPR EPN2 MRPL19
-5 -7 -6 -3 7 6 -7 -6 -7 7 -4 6 -3
TRAPPC3 STX4 IPO13 MNAT1 AGL LOXL1 CSNK2A2 RAB4A IGF1R FGFR2 HMOX1 NUCB2 BCL2
-7 7 7 -6 5 3 7 -5 -4 7 -5 4 6
FZD7 GADD45A BUB1B BLVRA SLC25A13 AKAP8 RAB21 RAP1GAP TCEA2 NFKBIE MRPL12 CEBPD WASF3
-6 7 7 -5 -5 -6 7 4 7 7 -7 7 4
PRKX SLC5A6 MAP3K4 AURKA CCNH TESK1 CDC45 FOXO3 IFNAR1 RTN2 GNA11 ELOVL6 PMAIP1
7 3 -7 -7 3 7 7 -4 7 7 -4 -5 7
PIK3CA GSTM2 FOSL1 FZD1 SNCA MMP1 PIK3C2B BID DPH2 BRCA1 ST6GALNAC2 IKBKE CGRRF1
6 5 -3 7 5 6 -4 6 -3 -7 3 6 -6
ACD TFAP2A KIAA0753 NCK1 PARP2 MAP2K5 C2CD2L USP6NL FAS PPOX TMEM5 CLPX ZW10
5 7 6 -7 -7 5 7 -6 -3 7 -5 -7 -4
MELK CCNF RAD9A ICAM3 TRAPPC6A CDK5R1 ATF5 LSM6 CENPE KIT ITGAE IL1B ORC1
-4 -7 -5 -5 7 5 -3 -5 -3 7 5 6 7
SGCB CD40 CLTB PLS1 PCMT1 GNA15 CBR3 CHEK1 SMAD3 PHKA1 FOXO4 PDGFA CASP10
3 7 6 3 -6 7 -3 -4 -6 5 -3 -7 7
C5 BTK RPP38 SNX7 NOS3 SCYL3 ALAS1 BPHL POLG2 HMGCS1 NOLC1 NFATC4 CCNA1
7 6 -7 7 5 -6 6 4 -4 -7 -5 7 5
POLE2 TBX2 FOXJ3 RAD51C EPHA3 FUT1 CRKL EGF KIF14 GLRX CPSF4 LPAR2 DFFB
-7 4 -5 4 3 7 5 6 -6 -7 6 4 6
SLC35A3 GLI2 CDKN2A E2F2 CASP7 TGFBR2 RAC2 POLR1C NFKB2 SYK TBXA2R GADD45B CASK
-3 6 3 7 -6 -6 4 3 4 5 6 3 -5
PSMD9 PROS1 CASC3 NVL PPARD CASP2 LSR EIF5 CBLB TBPL1 XPNPEP1 XPO7 BAX
4 3 -5 7 7 -5 7 -5 6 -4 -3 -6 6
SPTAN1 EIF4G1 VAT1 FDFT1 HSPA8 PDLIM1 OXA1L CDC42 HSPA4 ADH5 CYCS LGALS8 ALDH7A1
-3 4 -3 -4 -7 4 -5 -6 7 -3 5 7 7
DNAJB6 COPS7A PSMB8 CORO1A GLOD4 DLD IFRD2 CDKN1B PRPF4 MAN2B1 FOS TUBB6 CXCR4
6 6 -3 4 -7 -3 -3 -6 -6 7 7 -3 5
CBR1 SFN NR2F6 NSDHL IKBKB KIF2C AURKB RPA3 RAB27A GSTZ1 EED PRUNE EPHB2
3 -3 -4 -4 7 -6 6 -5 4 3 -6 -3 5
HIST1H2BK PUF60 ATP2C1 PRKCQ ZNF589 IGFBP3 RPL39L PLA2G4A CHEK2 GRB7 DHRS7 ERBB2 CDK7
3 -7 3 7 6 6 -3 7 -7 7 -3 -7 -7
BMP4 CDK19 VDAC1 WIPF2 HN1L PDS5A COG4 FBXO21 TMEM97 VGLL4 UBE3B SPRED2 GPATCH8
6 -4 -4 -4 -4 -5 7 3 -7 -5 7 7 -7
MAPK1IP1L ADO GAPDH CHN1 DHX29 TIPARP KDM3A PLEKHM1 PIK3R4 CAMSAP2 KIAA1033 ASCC3 SLC25A46
-7 -7 -3 4 -4 3 -7 7 -5 6 -7 -5 -6
RRP1B DCUN1D4 MAPKAPK5 C2CD2 WDR7 SUPV3L1 THAP11 RFNG APBB2 HOXA10 COG7 TICAM1 GDPD5
-7 3 -4 3 7 7 -4 6 6 -5 7 3 7
PLCB3 SPDEF FCHO1 NENF SOX2 HOXA5 TMEM110 NFKBIB ARID4B RALA ARPP19 CCNB1 RBM34
5 3 6 5 7 -3 7 6 -3 3 -5 -6 -5
DNM1 WDR61 AKAP8L IGHMBP2 PPP1R13B CCL2 NGRN ADI1 RAB31 TMEM50A YKT6 UBE2J1 EVL
4 -6 7 5 7 3 7 3 5 -3 -7 7 4
BACE2 PIH1D1 CAB39 IARS2 BAG3 LAP3 STUB1 ENOPH1 SQRDL MRPS2 NUP85 NUSAP1 MRPS16
6 6 -6 -5 -6 6 -3 -7 4 -7 -7 -6 -6
NPDC1 UBR7 TMEM2 ZNF395 ADCK3 ISOC1 CCDC92 GOLT1B SCAND1 NR1H2 TSKU ZDHHC6 TIMM9
6 -3 -5 7 -3 5 3 -4 -6 5 -5 -4 -7
GMNN CRELD2 NUDT9 CDCA4 CERK KCTD5 CD320 DHDDS SUV39H1 VPS28 NARFL CHMP6 KIF20A
6 7 -6 -7 7 6 5 7 -7 -6 7 6 -7
HOOK2 VAV3 SLC35F2 IGF2BP2 FAM57A NOTCH1 ANO10 FASTKD5 LAGE3 AMDHD2 PRR15L FSD1 TIMM22
3 6 -7 -4 -5 7 5 -6 3 4 7 7 7
RBKS CHAC1 MSRA ADAT1 FKBP14 CHIC2 PRR7 SPAG4 MCOLN1 SLC2A6 FBXL12 SNX11 ATG3
3 7 5 7 3 -3 6 4 7 -3 6 -7 -7
FAIM GTPBP8 PECR FRS2 BNIP3L GRWD1 ABHD6 SIRT3 STAP2 ACOT9 YTHDF1 MICALL1 FAM63A
5 -6 6 7 -6 -6 7 5 7 -7 -6 -7 5
P4HTM SLC27A3 MACF1 NPEPL1
6 6 -7 5
print("Check that genes are all in the right order... ")[1] "Check that genes are all in the right order... " head(rownames(overlap) == names(cmpd_ordered2))[1] TRUE TRUE TRUE TRUE TRUE TRUE
#
head(rownames(overlap))[1] "DDR1" "PAX8" "SCARB1" "PTPRC" "JMJD6" "TLR4" head(names(cmpd_ordered2))[1] "DDR1" "PAX8" "SCARB1" "PTPRC" "JMJD6" "TLR4" Now set up each different tumor type as a vector or whatever to be able to calculate SC for each…
# SHH
head(overlap)SHH <- overlap$Log2FC_SHH
names(SHH) <- rownames(overlap)
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")[1] "Check that genes are all in the right order... "head(names(SHH) == names(cmpd_ordered2))[1] TRUE TRUE TRUE TRUE TRUE TRUESC.SHH <- cor(cmpd_ordered2, SHH, method = "spearman")
# WNT
head(overlap)WNT <- overlap$Log2FC_WNT
names(WNT) <- rownames(overlap)
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")[1] "Check that genes are all in the right order... "head(names(WNT) == names(cmpd_ordered2))[1] TRUE TRUE TRUE TRUE TRUE TRUESC.WNT <- cor(cmpd_ordered2, WNT, method = "spearman")
# G3
head(overlap)G3 <- overlap$Log2FC_G3
names(G3) <- rownames(overlap)
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")[1] "Check that genes are all in the right order... "head(names(G3) == names(cmpd_ordered2))[1] TRUE TRUE TRUE TRUE TRUE TRUESC.G3 <- cor(cmpd_ordered2, G3, method = "spearman")
# G4
head(overlap)G4 <- overlap$Log2FC_G4
names(G4) <- rownames(overlap)
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")[1] "Check that genes are all in the right order... "head(names(G4) == names(cmpd_ordered2))[1] TRUE TRUE TRUE TRUE TRUE TRUESC.G4 <- cor(cmpd_ordered2, G4, method = "spearman")So how do we make a figure showing that g3 is predicted over SHH, others?
First, can we subset to a signature that we can visualize by thresholding on fold change?
G3 DDR1 PAX8 SCARB1 PTPRC JMJD6 TLR4 CNPY3 PIP4K2B SNX13 MBNL2
-0.0487913995 -0.0456389716 0.0671821998 -0.0601250512 0.0218637272 -0.0027584795 0.0154718710 -0.0025910950 0.0084135208 0.0113432566
MYO10 TXNDC9 DNAJA3 ATP5S CANT1 GNB5 TRAM2 FBXO7 CRTAP GFOD1
-0.0108054138 0.0061185887 0.0122281680 0.0577420351 0.0296763550 0.1271499568 -0.0024948390 0.0172462715 0.0529278086 -0.0043345685
ATP11B PSMD10 ARHGEF2 TOR1A PSIP1 FGFR4 PTGS2 LPGAT1 STAT5B TERT
0.0339939938 -0.0033599835 -0.0116381543 0.0099320197 -0.0485907715 0.0121498913 0.1358661365 0.0914431120 0.0024034206 0.0400260350
ETS1 ASAH1 RNH1 TGFB3 MBNL1 CDC25A RHEB TRIB3 CSNK1A1 SPEN
0.0455765383 -0.0021849718 -0.0283059245 0.0278543655 0.0092557947 0.0974301353 -0.0203703941 0.0620026195 0.0079036509 -0.0172002103
HOMER2 ITFG1 TSEN2 HEATR1 PHKG2 FAM69A COL1A1 SNAP25 RBM6 TCTN1
0.0221950810 -0.0340932090 0.0234017567 0.0624601626 -0.0530654267 0.0876332283 0.0639033184 0.0413275837 0.0251457060 -0.0230862630
BLCAP NT5DC2 SMC3 KIF5C G3BP1 MYCBP2 ZNF131 SHB PCCB GALE
-0.0596925965 0.0265246260 -0.0126004150 -0.0629647250 0.0224906783 0.0220867747 -0.0159616896 -0.0234346664 0.0172679810 -0.0125718987
CD44 CTNND1 ARID5B SRC ATF1 SYNE2 TPM1 SSBP2 MAP4K4 NOL3
0.0391607188 -0.0112518805 -0.0106911660 0.0103025376 0.0061149900 -0.0349941982 0.0629030915 -0.0411937117 -0.0355996470 -0.0341710010
RRP8 RRP12 KAT6A PTK2 ARHGEF12 TIMM17B DDX42 FKBP4 MKNK1 DYRK3
0.0371995690 -0.0119740532 0.0021422910 0.0332210545 -0.0037243458 0.0044308205 0.0151818017 0.0392512125 -0.0622793217 0.0272393535
RSU1 TXNRD1 TXLNA CCND3 NCOA3 CNDP2 DDX10 HERC6 INPP4B CAST
0.0348442020 -0.0054602055 0.0281651330 -0.0376397030 0.0299873562 -0.0328274480 0.0489106915 0.0730577500 -0.0102534287 0.0256840752
EDN1 EGFR TATDN2 PRSS23 IKZF1 SUZ12 KCNK1 MMP2 NFE2L2 SOX4
-0.1278627510 -0.1007566044 0.0245395600 -0.0357736805 -0.0119893693 0.0172974143 -0.1488072805 -0.0057805607 -0.0062287560 -0.0384272088
CHERP SERPINE1 IGF2R SMARCA4 TP53BP1 TRIM13 PRCP CCP110 PPP2R3C STXBP2
-0.0237510280 0.1047675547 0.0175329613 0.0220214716 0.0051658690 -0.0078431125 0.0045343412 0.0321315360 0.0085368607 -0.0142944105
BAD RPS5 ABCF1 SPAG7 RNPS1 SMNDC1 ATP6V0B RPS6 USP22 CLTC
-0.0242980633 0.0418646700 0.0361638410 0.0208820670 0.0010829485 0.0076570610 0.0343444160 0.0129438745 -0.0684802594 0.0303607217
CSRP1 PTPRF DNAJB1 XBP1 GRN HK1 CALU CTSD MAT2A GNAS
-0.0289263220 0.1314562600 0.0676783115 0.0354088515 -0.0427482113 -0.1219285910 0.0200435566 -0.0281243630 0.0237300105 0.0204870821
ECH1 IQGAP1 HSPA1A HSPD1 PAFAH1B1 HYOU1 PSMD2 EPRS PSMD4 TMED10
0.0050745620 0.0386016013 0.0245368413 0.0491196886 0.0360722770 -0.0045511980 -0.0147643630 0.0583034673 0.0402127935 0.0301930393
HIF1A PAICS PSMF1 MYL9 SMARCC1 TM9SF2 PXN COPB2 PFKL ITGB5
-0.0027407920 0.0710722713 0.0049828038 0.0164958505 0.0356057590 0.0389588440 -0.0198596940 0.0078831495 -0.0280452660 -0.0135798330
ACLY PLP2 BHLHE40 TERF2IP HTRA1 LRPAP1 CREG1 PCNA LGMN ATP1B1
0.0598630563 0.1206142090 -0.0181385460 -0.0685826230 -0.0933477130 0.0041991830 -0.0188762570 0.0331951580 0.0314705190 0.0595998550
SYPL1 NUDCD3 TOP2A EBNA1BP2 SCP2 ANXA7 TPD52L2 TRAP1 CAT MAPKAPK2
0.0140339560 -0.0595639817 0.0632546870 0.0374547680 0.0607202640 -0.0056094300 -0.0179389010 -0.0455588500 -0.0061536153 -0.0733902277
JUN SHC1 SQSTM1 USP7 NFKBIA TOMM70A ZFP36 KDM5B MCM3 RAE1
0.0617870627 0.0182114755 -0.0302412523 -0.0187025070 0.0663207360 0.1033180165 -0.0978937550 0.0144580724 0.0203954360 -0.0158568543
CLIC4 ID2 NISCH PWP1 RUVBL1 MBTPS1 INSIG1 RRAGA IER3 UBE2L6
0.0379038180 0.0405363615 0.0763931440 0.0180408903 0.0248210410 -0.0599090065 0.0054039438 -0.0624999190 0.0146784020 -0.1124652210
SMC4 USP14 PNP DNMT1 MYBL2 RPA2 MTHFD2 DAXX ELAC2 NCAPD2
0.0711149053 0.0188244610 0.0689846150 0.0393505820 0.1086395350 -0.0030789480 0.0997487690 0.0072002770 -0.0076372625 0.0415195860
LBR SCCPDH NET1 HDAC2 BNIP3 CDC25B ATMIN MPZL1 IL13RA1 PSRC1
0.0016582240 0.0178712280 0.0096862890 0.0012021520 -0.0090135090 0.0069597080 -0.0616725580 0.0014480237 -0.0243491725 -0.0628945730
PGM1 KIAA0196 EXT1 PTPN12 TWF2 TJP1 MEST ALDOC ACAA1 KDM5A
-0.0898818470 0.0395921920 0.0079204933 0.0055204990 -0.0613615960 -0.0198833890 -0.0477617650 -0.2632686900 -0.0022367505 0.0083126624
RAI14 BIRC2 PAF1 RALB ARFIP2 ARHGAP1 CPNE3 ABL1 TRAK2 NUP62
-0.0084580160 0.0026388660 -0.0370873620 0.0303013325 0.0073244900 -0.0363666817 0.0448785945 -0.0031702500 0.1188727050 -0.0155467227
PCM1 BLMH MVP PLOD3 ARL4C KIAA0907 CRK PLK1 CDK4 MTA1
0.0493880670 0.0378235920 -0.0308943890 -0.0154721620 -0.0511524302 0.0541267885 0.0269962133 0.0431637310 0.0006805000 0.0164722705
STXBP1 VPS72 FEZ2 SENP6 ACBD3 CSK CSNK1E TRIM2 RGS2 ABCF3
-0.0786880890 -0.0211930710 0.0684414280 -0.0020569627 0.0075083425 -0.0379082670 -0.0284993990 -0.0549893183 0.0639930700 -0.0004122800
TCERG1 USP1 MYC SLC35B1 DECR1 PAPD7 H2AFV IKBKAP BCL7B HMGCR
0.0449700223 0.0054634865 0.4261564470 0.0349244910 -0.0496953110 -0.0039645600 -0.0293456115 -0.0180228085 0.0049291950 0.0649062065
NRIP1 HTATSF1 ADAM10 EAPP LYN APPBP2 POLR2K ICAM1 PSMB10 SDHB
0.0146296410 -0.0034657545 0.0150399656 -0.0010762830 -0.1521439300 -0.0226747180 0.0864680700 -0.0284914557 -0.1004491850 0.0401067590
RASA1 GTF2A2 NPC1 GTF2E2 RNMT RBM15B OXSR1 DUSP11 CCNB2 HIST2H2BE
0.0102267055 0.0208596643 -0.0169537902 0.0339688180 -0.0055300275 0.0029150010 0.0102668500 0.0056611960 -0.0716007450 0.0370291620
PTPN1 TES EBP PHKB PIK3R3 WRB GPC1 CASP3 DNTTIP2 ZMYM2
0.0041042418 -0.0598638523 0.0461429310 -0.0509563675 0.0349836620 0.0003100470 -0.0531062870 0.0067878890 0.0233123100 0.0304811319
OXCT1 MAPKAPK3 INPP1 SACM1L PRKACA INTS3 STAMBP GAA TARBP1 SLC37A4
-0.0123781090 -0.0420204190 -0.0520295680 0.0479078350 -0.0106772110 0.0009519780 0.0122075807 -0.0861673290 -0.0072398350 0.0613654825
PCK2 FAH POP4 CDC20 CYTH1 NIT1 NUP88 LSM5 MSH6 FAM20B
0.1925205080 -0.0226648665 0.0072525950 0.0850953490 -0.0408102610 -0.0066087260 0.0251438885 0.0298526821 -0.0071003897 0.0794342415
FHL2 CRYZ UBE2C RFX5 ARNT2 POLD4 LYPLA1 ECD PTPRK TIMELESS
-0.0463779680 0.1492747130 0.0355885250 0.0553355320 -0.0790274060 -0.0167739480 0.1457716265 0.0318681920 -0.2782815455 -0.0091321410
STK10 TCTA PDHX PTK2B TP53BP2 SLC11A2 SPTLC2 TBP HAT1 TIMP2
-0.0072698270 0.0319208060 0.0361207050 -0.1000499355 -0.0088880050 0.0218464846 0.0373247476 -0.0048597700 0.0460268700 0.0037885430
PMM2 MTFR1 CDK1 ST3GAL5 MAPK9 TLE1 IL4R NPRL2 FBXO11 CDH3
0.0512669700 0.0929995660 0.0295286423 -0.0096539650 -0.0360034040 -0.2104426214 0.0100097050 -0.0285424320 -0.0103206912 -0.3558887030
DFFA EDEM1 HS2ST1 KIAA0355 CNOT4 DMTF1 DCK BAMBI NCK2 IDE
0.0365565933 0.0163508060 0.0426744190 -0.0218880410 -0.0002025818 0.0086796370 -0.0087063860 -0.0358097550 -0.0635844930 0.0480001577
PPP2R5E CEBPZ MTF2 EZH2 DUSP14 SOCS2 APOE PSMG1 DDB2 CCNA2
0.0292587112 0.0250261900 0.0238005616 -0.0244844470 0.0050371790 -0.1199871803 -0.0799151148 0.1374729900 -0.0066459520 0.0602552180
EML3 SPR EPN2 MRPL19 TRAPPC3 STX4 IPO13 MNAT1 AGL LOXL1
-0.0218988256 0.0358713790 -0.0423238010 0.0475340163 0.0156739170 0.0045477390 -0.0043635900 0.0360090860 0.0194218190 0.1454031580
CSNK2A2 RAB4A IGF1R FGFR2 HMOX1 NUCB2 BCL2 FZD7 GADD45A BUB1B
0.0209286365 0.0321262143 0.0381824546 0.0058611016 -0.0360414410 0.0105821040 0.0220775573 0.1659426030 0.0927515300 0.1017785420
BLVRA SLC25A13 AKAP8 RAB21 RAP1GAP TCEA2 NFKBIE MRPL12 CEBPD WASF3
0.0004777544 -0.0065798253 0.0166237495 0.0289916775 0.0466771485 -0.1103100913 -0.0450364730 0.0048064920 0.0031264550 0.0349280090
PRKX SLC5A6 MAP3K4 AURKA CCNH TESK1 CDC45 FOXO3 IFNAR1 RTN2
-0.1260799940 0.1094041140 0.0773074755 0.0640982363 -0.0300515610 -0.0274854530 0.0220929060 -0.0403288266 -0.0480499195 -0.0178101380
GNA11 ELOVL6 PMAIP1 PIK3CA GSTM2 FOSL1 FZD1 SNCA MMP1 PIK3C2B
-0.0293040742 -0.0339570957 -0.0613600785 -0.0417947877 -0.0201982280 -0.0627816770 0.1762483483 -0.2755466862 0.0708894660 -0.0612959910
BID DPH2 BRCA1 ST6GALNAC2 IKBKE CGRRF1 ACD TFAP2A KIAA0753 NCK1
-0.0134585653 0.0174793530 -0.0073485635 0.0334383480 0.0131955425 0.0079485660 -0.1070586140 -0.0104502487 0.0226208500 0.0090977902
PARP2 MAP2K5 C2CD2L USP6NL FAS PPOX TMEM5 CLPX ZW10 MELK
0.0181871887 -0.0259556635 0.0468601725 0.0394232927 -0.0642531238 0.0001677213 0.0010082140 0.0182277220 0.0655491440 0.0554313500
CCNF RAD9A ICAM3 TRAPPC6A CDK5R1 ATF5 LSM6 CENPE KIT ITGAE
0.0910164000 -0.0398008800 -0.1171768820 -0.0507576210 -0.0401874820 0.0366278757 0.0291714310 0.0960813850 0.0557225050 0.0394208660
IL1B ORC1 SGCB CD40 CLTB PLS1 PCMT1 GNA15 CBR3 CHEK1
-0.0634881170 0.0192622850 -0.0741192253 -0.0163640265 -0.0400246417 0.0954317550 0.0203483473 -0.0095179040 -0.1874947770 0.0638720947
SMAD3 PHKA1 FOXO4 PDGFA CASP10 C5 BTK RPP38 SNX7 NOS3
0.0265305207 0.0090868115 -0.0132118640 -0.0488589120 -0.0139226063 -0.1664309980 -0.0433042490 0.0326883670 0.0762309600 0.2551925070
SCYL3 ALAS1 BPHL POLG2 HMGCS1 NOLC1 NFATC4 CCNA1 POLE2 TBX2
0.0206822360 0.0140141640 -0.0481556010 0.0144717770 0.0343635995 0.0200803193 -0.0344002043 -0.0606241650 0.0612519160 -0.0177039720
FOXJ3 RAD51C EPHA3 FUT1 CRKL EGF KIF14 GLRX CPSF4 LPAR2
0.0047537745 0.0375387645 -0.0020513613 -0.0314414070 0.0167465915 0.0370524820 0.1121642050 0.0147019070 0.0028355780 -0.0414470750
DFFB SLC35A3 GLI2 CDKN2A E2F2 CASP7 TGFBR2 RAC2 POLR1C NFKB2
0.0419555390 -0.0053591393 -0.0429800967 -0.0310670937 0.0557267883 -0.0400631390 0.0535987400 -0.0728361715 0.0671416890 -0.0436350183
SYK TBXA2R GADD45B CASK PSMD9 PROS1 CASC3 NVL PPARD CASP2
0.3033506405 0.0052436170 0.0002465720 0.0018948756 0.0414859960 -0.0214299510 -0.0466005970 0.0388635120 -0.0186341788 0.0017548894
LSR EIF5 CBLB TBPL1 XPNPEP1 XPO7 BAX SPTAN1 EIF4G1 VAT1
-0.0493698040 0.0184341866 0.0961424887 -0.0009599480 0.0243466713 0.0352471600 0.0163260005 -0.0222047438 0.0365872855 -0.0683949740
FDFT1 HSPA8 PDLIM1 OXA1L CDC42 HSPA4 ADH5 CYCS LGALS8 ALDH7A1
0.0597294020 0.0275706198 0.1391876200 0.0651224640 0.0261411392 0.0631597640 0.0039192185 -0.0015603430 0.0440354662 -0.0077360377
DNAJB6 COPS7A PSMB8 CORO1A GLOD4 DLD IFRD2 CDKN1B PRPF4 MAN2B1
0.0400052450 -0.0120776940 0.2495461400 -0.1049919910 -0.0273326700 0.0502410805 0.0357135240 0.0048221350 0.0151667355 0.0168853090
FOS TUBB6 CXCR4 CBR1 SFN NR2F6 NSDHL IKBKB KIF2C AURKB
-0.0458717540 -0.0156289180 0.0365443747 0.0138730190 -0.0218581960 0.0678360577 0.0299633965 0.0284543967 0.0830795220 0.0859259190
RPA3 RAB27A GSTZ1 EED PRUNE EPHB2 HIST1H2BK PUF60 ATP2C1 PRKCQ
0.0530351240 -0.0115720332 0.0335273790 0.0539727110 0.0350543710 -0.0394641054 0.0520147260 0.0134849040 0.0735162547 0.0404867330
ZNF589 IGFBP3 RPL39L PLA2G4A CHEK2 GRB7 DHRS7 ERBB2 CDK7 BMP4
0.0191211817 0.0622789575 -0.0622300040 0.0198653090 0.0262729950 -0.0181197410 0.0233031007 -0.0662874033 0.0535293980 -0.0292045400
CDK19 VDAC1 WIPF2 HN1L PDS5A COG4 FBXO21 TMEM97 VGLL4 UBE3B
-0.0344775352 0.0083247847 -0.0226782168 0.0004037753 0.0363618365 -0.0958521790 -0.0329883257 0.0322847110 -0.1245172805 0.0157846815
SPRED2 GPATCH8 MAPK1IP1L ADO GAPDH CHN1 DHX29 TIPARP KDM3A PLEKHM1
0.0151260123 -0.0072624850 0.0106710925 -0.0091692450 0.0140014782 -0.1051355390 0.0242384140 0.0502487700 0.0909427235 -0.0115925455
PIK3R4 CAMSAP2 KIAA1033 ASCC3 SLC25A46 RRP1B DCUN1D4 MAPKAPK5 C2CD2 WDR7
0.0066291107 0.0156960267 0.0282974337 0.0646515990 0.0008534460 0.0414089075 -0.0232097217 0.0383117845 0.0402856280 -0.0208450395
SUPV3L1 THAP11 RFNG APBB2 HOXA10 COG7 TICAM1 GDPD5 PLCB3 SPDEF
-0.0134663710 -0.0305872650 -0.0504759670 0.0288108216 0.0128787805 -0.0476206770 0.1201310820 0.0793159285 0.0333728450 0.0423500932
FCHO1 NENF SOX2 HOXA5 TMEM110 NFKBIB ARID4B RALA ARPP19 CCNB1
-0.0118323900 0.0141299525 -0.0611985997 0.0788659540 0.0313531060 -0.0021516990 0.0259249195 0.0206823150 0.0093898023 0.0680331705
RBM34 DNM1 WDR61 AKAP8L IGHMBP2 PPP1R13B CCL2 NGRN ADI1 RAB31
-0.0290578820 -0.1018115985 0.0028901950 0.0370965048 0.0132725483 0.0162129180 0.1424147770 0.0036667283 0.0074927940 -0.0780890207
TMEM50A YKT6 UBE2J1 EVL BACE2 PIH1D1 CAB39 IARS2 BAG3 LAP3
0.0210497625 0.0159397940 0.0731200617 0.0074057920 -0.0245869113 -0.0037112750 0.0043392200 0.0586633540 -0.0359330670 0.0353684010
STUB1 ENOPH1 SQRDL MRPS2 NUP85 NUSAP1 MRPS16 NPDC1 UBR7 TMEM2
-0.0398094837 0.0312823140 -0.0533107540 0.0075857010 0.0125252420 0.0617493280 0.0217226125 -0.0484566490 0.0221665760 -0.0259300750
ZNF395 ADCK3 ISOC1 CCDC92 GOLT1B SCAND1 NR1H2 TSKU ZDHHC6 TIMM9
0.0506821433 0.0122316590 0.1764540910 -0.0495760880 0.0397577700 -0.0215070780 -0.0889810660 0.0496492150 0.0052835320 0.0600677870
GMNN CRELD2 NUDT9 CDCA4 CERK KCTD5 CD320 DHDDS SUV39H1 VPS28
0.0073228080 0.0206527410 0.0265541420 0.0547367810 -0.0696747570 -0.0171017393 0.0753358300 -0.0545451985 -0.0061926660 -0.0089665520
NARFL CHMP6 KIF20A HOOK2 VAV3 SLC35F2 IGF2BP2 FAM57A NOTCH1 ANO10
-0.0755056980 -0.0538229850 0.0737769920 0.0225532420 0.0052280440 0.0006165820 0.0289402380 -0.0328129570 0.0534230790 -0.0043653940
FASTKD5 LAGE3 AMDHD2 PRR15L FSD1 TIMM22 RBKS CHAC1 MSRA ADAT1
0.0275351460 -0.0140379190 -0.1922636650 0.0347196440 -0.1779230860 -0.0020847937 0.0737755380 0.0236545150 -0.1316496870 -0.0718148460
FKBP14 CHIC2 PRR7 SPAG4 MCOLN1 SLC2A6 FBXL12 SNX11 ATG3 FAIM
0.0170483917 -0.0017746890 0.0211565820 0.0658832550 -0.0060871320 0.1017468040 0.0026517195 0.0182990100 0.0222526545 0.0785146920
GTPBP8 PECR FRS2 BNIP3L GRWD1 ABHD6 SIRT3 STAP2 ACOT9 YTHDF1
-0.0086561470 -0.0065644375 0.0047739027 0.0021209925 0.0377533780 -0.0540747987 -0.0033130537 0.0137236800 0.0332240610 -0.0083579240
MICALL1 FAM63A P4HTM SLC27A3 MACF1 NPEPL1
0.0310617985 -0.0696536875 -0.0077015290 -0.1012534970 -0.0296154260 0.0172414015 df <- as.data.frame(G3)
df G3
DDR1 -0.0487913995
PAX8 -0.0456389716
SCARB1 0.0671821998
PTPRC -0.0601250512
JMJD6 0.0218637272
TLR4 -0.0027584795
CNPY3 0.0154718710
PIP4K2B -0.0025910950
SNX13 0.0084135208
MBNL2 0.0113432566
MYO10 -0.0108054138
TXNDC9 0.0061185887
DNAJA3 0.0122281680
ATP5S 0.0577420351
CANT1 0.0296763550
GNB5 0.1271499568
TRAM2 -0.0024948390
FBXO7 0.0172462715
CRTAP 0.0529278086
GFOD1 -0.0043345685
ATP11B 0.0339939938
PSMD10 -0.0033599835
ARHGEF2 -0.0116381543
TOR1A 0.0099320197
PSIP1 -0.0485907715
FGFR4 0.0121498913
PTGS2 0.1358661365
LPGAT1 0.0914431120
STAT5B 0.0024034206
TERT 0.0400260350
ETS1 0.0455765383
ASAH1 -0.0021849718
RNH1 -0.0283059245
TGFB3 0.0278543655
MBNL1 0.0092557947
CDC25A 0.0974301353
RHEB -0.0203703941
TRIB3 0.0620026195
CSNK1A1 0.0079036509
SPEN -0.0172002103
HOMER2 0.0221950810
ITFG1 -0.0340932090
TSEN2 0.0234017567
HEATR1 0.0624601626
PHKG2 -0.0530654267
FAM69A 0.0876332283
COL1A1 0.0639033184
SNAP25 0.0413275837
RBM6 0.0251457060
TCTN1 -0.0230862630
BLCAP -0.0596925965
NT5DC2 0.0265246260
SMC3 -0.0126004150
KIF5C -0.0629647250
G3BP1 0.0224906783
MYCBP2 0.0220867747
ZNF131 -0.0159616896
SHB -0.0234346664
PCCB 0.0172679810
GALE -0.0125718987
CD44 0.0391607188
CTNND1 -0.0112518805
ARID5B -0.0106911660
SRC 0.0103025376
ATF1 0.0061149900
SYNE2 -0.0349941982
TPM1 0.0629030915
SSBP2 -0.0411937117
MAP4K4 -0.0355996470
NOL3 -0.0341710010
RRP8 0.0371995690
RRP12 -0.0119740532
KAT6A 0.0021422910
PTK2 0.0332210545
ARHGEF12 -0.0037243458
TIMM17B 0.0044308205
DDX42 0.0151818017
FKBP4 0.0392512125
MKNK1 -0.0622793217
DYRK3 0.0272393535
RSU1 0.0348442020
TXNRD1 -0.0054602055
TXLNA 0.0281651330
CCND3 -0.0376397030
NCOA3 0.0299873562
CNDP2 -0.0328274480
DDX10 0.0489106915
HERC6 0.0730577500
INPP4B -0.0102534287
CAST 0.0256840752
EDN1 -0.1278627510
EGFR -0.1007566044
TATDN2 0.0245395600
PRSS23 -0.0357736805
IKZF1 -0.0119893693
SUZ12 0.0172974143
KCNK1 -0.1488072805
MMP2 -0.0057805607
NFE2L2 -0.0062287560
SOX4 -0.0384272088
CHERP -0.0237510280
SERPINE1 0.1047675547
IGF2R 0.0175329613
SMARCA4 0.0220214716
TP53BP1 0.0051658690
TRIM13 -0.0078431125
PRCP 0.0045343412
CCP110 0.0321315360
PPP2R3C 0.0085368607
STXBP2 -0.0142944105
BAD -0.0242980633
RPS5 0.0418646700
ABCF1 0.0361638410
SPAG7 0.0208820670
RNPS1 0.0010829485
SMNDC1 0.0076570610
ATP6V0B 0.0343444160
RPS6 0.0129438745
USP22 -0.0684802594
CLTC 0.0303607217
CSRP1 -0.0289263220
PTPRF 0.1314562600
DNAJB1 0.0676783115
XBP1 0.0354088515
GRN -0.0427482113
HK1 -0.1219285910
CALU 0.0200435566
CTSD -0.0281243630
MAT2A 0.0237300105
GNAS 0.0204870821
ECH1 0.0050745620
IQGAP1 0.0386016013
HSPA1A 0.0245368413
HSPD1 0.0491196886
PAFAH1B1 0.0360722770
HYOU1 -0.0045511980
PSMD2 -0.0147643630
EPRS 0.0583034673
PSMD4 0.0402127935
TMED10 0.0301930393
HIF1A -0.0027407920
PAICS 0.0710722713
PSMF1 0.0049828038
MYL9 0.0164958505
SMARCC1 0.0356057590
TM9SF2 0.0389588440
PXN -0.0198596940
COPB2 0.0078831495
PFKL -0.0280452660
ITGB5 -0.0135798330
ACLY 0.0598630563
PLP2 0.1206142090
BHLHE40 -0.0181385460
TERF2IP -0.0685826230
HTRA1 -0.0933477130
LRPAP1 0.0041991830
CREG1 -0.0188762570
PCNA 0.0331951580
LGMN 0.0314705190
ATP1B1 0.0595998550
SYPL1 0.0140339560
NUDCD3 -0.0595639817
TOP2A 0.0632546870
EBNA1BP2 0.0374547680
SCP2 0.0607202640
ANXA7 -0.0056094300
TPD52L2 -0.0179389010
TRAP1 -0.0455588500
CAT -0.0061536153
MAPKAPK2 -0.0733902277
JUN 0.0617870627
SHC1 0.0182114755
SQSTM1 -0.0302412523
USP7 -0.0187025070
NFKBIA 0.0663207360
TOMM70A 0.1033180165
ZFP36 -0.0978937550
KDM5B 0.0144580724
MCM3 0.0203954360
RAE1 -0.0158568543
CLIC4 0.0379038180
ID2 0.0405363615
NISCH 0.0763931440
PWP1 0.0180408903
RUVBL1 0.0248210410
MBTPS1 -0.0599090065
INSIG1 0.0054039438
RRAGA -0.0624999190
IER3 0.0146784020
UBE2L6 -0.1124652210
SMC4 0.0711149053
USP14 0.0188244610
PNP 0.0689846150
DNMT1 0.0393505820
MYBL2 0.1086395350
RPA2 -0.0030789480
MTHFD2 0.0997487690
DAXX 0.0072002770
ELAC2 -0.0076372625
NCAPD2 0.0415195860
LBR 0.0016582240
SCCPDH 0.0178712280
NET1 0.0096862890
HDAC2 0.0012021520
BNIP3 -0.0090135090
CDC25B 0.0069597080
ATMIN -0.0616725580
MPZL1 0.0014480237
IL13RA1 -0.0243491725
PSRC1 -0.0628945730
PGM1 -0.0898818470
KIAA0196 0.0395921920
EXT1 0.0079204933
PTPN12 0.0055204990
TWF2 -0.0613615960
TJP1 -0.0198833890
MEST -0.0477617650
ALDOC -0.2632686900
ACAA1 -0.0022367505
KDM5A 0.0083126624
RAI14 -0.0084580160
BIRC2 0.0026388660
PAF1 -0.0370873620
RALB 0.0303013325
ARFIP2 0.0073244900
ARHGAP1 -0.0363666817
CPNE3 0.0448785945
ABL1 -0.0031702500
TRAK2 0.1188727050
NUP62 -0.0155467227
PCM1 0.0493880670
BLMH 0.0378235920
MVP -0.0308943890
PLOD3 -0.0154721620
ARL4C -0.0511524302
KIAA0907 0.0541267885
CRK 0.0269962133
PLK1 0.0431637310
CDK4 0.0006805000
MTA1 0.0164722705
STXBP1 -0.0786880890
VPS72 -0.0211930710
FEZ2 0.0684414280
SENP6 -0.0020569627
ACBD3 0.0075083425
CSK -0.0379082670
CSNK1E -0.0284993990
TRIM2 -0.0549893183
RGS2 0.0639930700
ABCF3 -0.0004122800
TCERG1 0.0449700223
USP1 0.0054634865
MYC 0.4261564470
SLC35B1 0.0349244910
DECR1 -0.0496953110
PAPD7 -0.0039645600
H2AFV -0.0293456115
IKBKAP -0.0180228085
BCL7B 0.0049291950
HMGCR 0.0649062065
NRIP1 0.0146296410
HTATSF1 -0.0034657545
ADAM10 0.0150399656
EAPP -0.0010762830
LYN -0.1521439300
APPBP2 -0.0226747180
POLR2K 0.0864680700
ICAM1 -0.0284914557
PSMB10 -0.1004491850
SDHB 0.0401067590
RASA1 0.0102267055
GTF2A2 0.0208596643
NPC1 -0.0169537902
GTF2E2 0.0339688180
RNMT -0.0055300275
RBM15B 0.0029150010
OXSR1 0.0102668500
DUSP11 0.0056611960
CCNB2 -0.0716007450
HIST2H2BE 0.0370291620
PTPN1 0.0041042418
TES -0.0598638523
EBP 0.0461429310
PHKB -0.0509563675
PIK3R3 0.0349836620
WRB 0.0003100470
GPC1 -0.0531062870
CASP3 0.0067878890
DNTTIP2 0.0233123100
ZMYM2 0.0304811319
OXCT1 -0.0123781090
MAPKAPK3 -0.0420204190
INPP1 -0.0520295680
SACM1L 0.0479078350
PRKACA -0.0106772110
INTS3 0.0009519780
STAMBP 0.0122075807
GAA -0.0861673290
TARBP1 -0.0072398350
SLC37A4 0.0613654825
PCK2 0.1925205080
FAH -0.0226648665
POP4 0.0072525950
CDC20 0.0850953490
CYTH1 -0.0408102610
NIT1 -0.0066087260
NUP88 0.0251438885
LSM5 0.0298526821
MSH6 -0.0071003897
FAM20B 0.0794342415
FHL2 -0.0463779680
CRYZ 0.1492747130
UBE2C 0.0355885250
RFX5 0.0553355320
ARNT2 -0.0790274060
POLD4 -0.0167739480
LYPLA1 0.1457716265
ECD 0.0318681920
PTPRK -0.2782815455
TIMELESS -0.0091321410
STK10 -0.0072698270
TCTA 0.0319208060
PDHX 0.0361207050
PTK2B -0.1000499355
TP53BP2 -0.0088880050
SLC11A2 0.0218464846
SPTLC2 0.0373247476
TBP -0.0048597700
HAT1 0.0460268700
TIMP2 0.0037885430
PMM2 0.0512669700
MTFR1 0.0929995660
CDK1 0.0295286423
ST3GAL5 -0.0096539650
MAPK9 -0.0360034040
TLE1 -0.2104426214
IL4R 0.0100097050
NPRL2 -0.0285424320
FBXO11 -0.0103206912
CDH3 -0.3558887030
DFFA 0.0365565933
EDEM1 0.0163508060
HS2ST1 0.0426744190
KIAA0355 -0.0218880410
CNOT4 -0.0002025818
DMTF1 0.0086796370
DCK -0.0087063860
BAMBI -0.0358097550
NCK2 -0.0635844930
IDE 0.0480001577
PPP2R5E 0.0292587112
CEBPZ 0.0250261900
MTF2 0.0238005616
EZH2 -0.0244844470
DUSP14 0.0050371790
SOCS2 -0.1199871803
APOE -0.0799151148
PSMG1 0.1374729900
DDB2 -0.0066459520
CCNA2 0.0602552180
EML3 -0.0218988256
SPR 0.0358713790
EPN2 -0.0423238010
MRPL19 0.0475340163
TRAPPC3 0.0156739170
STX4 0.0045477390
IPO13 -0.0043635900
MNAT1 0.0360090860
AGL 0.0194218190
LOXL1 0.1454031580
CSNK2A2 0.0209286365
RAB4A 0.0321262143
IGF1R 0.0381824546
FGFR2 0.0058611016
HMOX1 -0.0360414410
NUCB2 0.0105821040
BCL2 0.0220775573
FZD7 0.1659426030
GADD45A 0.0927515300
BUB1B 0.1017785420
BLVRA 0.0004777544
SLC25A13 -0.0065798253
AKAP8 0.0166237495
RAB21 0.0289916775
RAP1GAP 0.0466771485
TCEA2 -0.1103100913
NFKBIE -0.0450364730
MRPL12 0.0048064920
CEBPD 0.0031264550
WASF3 0.0349280090
PRKX -0.1260799940
SLC5A6 0.1094041140
MAP3K4 0.0773074755
AURKA 0.0640982363
CCNH -0.0300515610
TESK1 -0.0274854530
CDC45 0.0220929060
FOXO3 -0.0403288266
IFNAR1 -0.0480499195
RTN2 -0.0178101380
GNA11 -0.0293040742
ELOVL6 -0.0339570957
PMAIP1 -0.0613600785
PIK3CA -0.0417947877
GSTM2 -0.0201982280
FOSL1 -0.0627816770
FZD1 0.1762483483
SNCA -0.2755466862
MMP1 0.0708894660
PIK3C2B -0.0612959910
BID -0.0134585653
DPH2 0.0174793530
BRCA1 -0.0073485635
ST6GALNAC2 0.0334383480
IKBKE 0.0131955425
CGRRF1 0.0079485660
ACD -0.1070586140
TFAP2A -0.0104502487
KIAA0753 0.0226208500
NCK1 0.0090977902
PARP2 0.0181871887
MAP2K5 -0.0259556635
C2CD2L 0.0468601725
USP6NL 0.0394232927
FAS -0.0642531238
PPOX 0.0001677213
TMEM5 0.0010082140
CLPX 0.0182277220
ZW10 0.0655491440
MELK 0.0554313500
CCNF 0.0910164000
RAD9A -0.0398008800
ICAM3 -0.1171768820
TRAPPC6A -0.0507576210
CDK5R1 -0.0401874820
ATF5 0.0366278757
LSM6 0.0291714310
CENPE 0.0960813850
KIT 0.0557225050
ITGAE 0.0394208660
IL1B -0.0634881170
ORC1 0.0192622850
SGCB -0.0741192253
CD40 -0.0163640265
CLTB -0.0400246417
PLS1 0.0954317550
PCMT1 0.0203483473
GNA15 -0.0095179040
CBR3 -0.1874947770
CHEK1 0.0638720947
SMAD3 0.0265305207
PHKA1 0.0090868115
FOXO4 -0.0132118640
PDGFA -0.0488589120
CASP10 -0.0139226063
C5 -0.1664309980
BTK -0.0433042490
RPP38 0.0326883670
SNX7 0.0762309600
NOS3 0.2551925070
SCYL3 0.0206822360
ALAS1 0.0140141640
BPHL -0.0481556010
POLG2 0.0144717770
HMGCS1 0.0343635995
NOLC1 0.0200803193
NFATC4 -0.0344002043
CCNA1 -0.0606241650
POLE2 0.0612519160
TBX2 -0.0177039720
FOXJ3 0.0047537745
RAD51C 0.0375387645
EPHA3 -0.0020513613
FUT1 -0.0314414070
CRKL 0.0167465915
EGF 0.0370524820
KIF14 0.1121642050
GLRX 0.0147019070
CPSF4 0.0028355780
LPAR2 -0.0414470750
DFFB 0.0419555390
SLC35A3 -0.0053591393
GLI2 -0.0429800967
CDKN2A -0.0310670937
E2F2 0.0557267883
CASP7 -0.0400631390
TGFBR2 0.0535987400
RAC2 -0.0728361715
POLR1C 0.0671416890
NFKB2 -0.0436350183
SYK 0.3033506405
TBXA2R 0.0052436170
GADD45B 0.0002465720
CASK 0.0018948756
PSMD9 0.0414859960
PROS1 -0.0214299510
CASC3 -0.0466005970
NVL 0.0388635120
PPARD -0.0186341788
CASP2 0.0017548894
LSR -0.0493698040
EIF5 0.0184341866
CBLB 0.0961424887
TBPL1 -0.0009599480
XPNPEP1 0.0243466713
XPO7 0.0352471600
BAX 0.0163260005
SPTAN1 -0.0222047438
EIF4G1 0.0365872855
VAT1 -0.0683949740
FDFT1 0.0597294020
HSPA8 0.0275706198
PDLIM1 0.1391876200
OXA1L 0.0651224640
CDC42 0.0261411392
HSPA4 0.0631597640
ADH5 0.0039192185
CYCS -0.0015603430
LGALS8 0.0440354662
ALDH7A1 -0.0077360377
DNAJB6 0.0400052450
COPS7A -0.0120776940
PSMB8 0.2495461400
CORO1A -0.1049919910
GLOD4 -0.0273326700
DLD 0.0502410805
IFRD2 0.0357135240
CDKN1B 0.0048221350
PRPF4 0.0151667355
MAN2B1 0.0168853090
FOS -0.0458717540
TUBB6 -0.0156289180
CXCR4 0.0365443747
CBR1 0.0138730190
SFN -0.0218581960
NR2F6 0.0678360577
NSDHL 0.0299633965
IKBKB 0.0284543967
KIF2C 0.0830795220
AURKB 0.0859259190
RPA3 0.0530351240
RAB27A -0.0115720332
GSTZ1 0.0335273790
EED 0.0539727110
PRUNE 0.0350543710
EPHB2 -0.0394641054
HIST1H2BK 0.0520147260
PUF60 0.0134849040
ATP2C1 0.0735162547
PRKCQ 0.0404867330
ZNF589 0.0191211817
IGFBP3 0.0622789575
RPL39L -0.0622300040
PLA2G4A 0.0198653090
CHEK2 0.0262729950
GRB7 -0.0181197410
DHRS7 0.0233031007
ERBB2 -0.0662874033
CDK7 0.0535293980
BMP4 -0.0292045400
CDK19 -0.0344775352
VDAC1 0.0083247847
WIPF2 -0.0226782168
HN1L 0.0004037753
PDS5A 0.0363618365
COG4 -0.0958521790
FBXO21 -0.0329883257
TMEM97 0.0322847110
VGLL4 -0.1245172805
UBE3B 0.0157846815
SPRED2 0.0151260123
GPATCH8 -0.0072624850
MAPK1IP1L 0.0106710925
ADO -0.0091692450
GAPDH 0.0140014782
CHN1 -0.1051355390
DHX29 0.0242384140
TIPARP 0.0502487700
KDM3A 0.0909427235
PLEKHM1 -0.0115925455
PIK3R4 0.0066291107
CAMSAP2 0.0156960267
KIAA1033 0.0282974337
ASCC3 0.0646515990
SLC25A46 0.0008534460
RRP1B 0.0414089075
DCUN1D4 -0.0232097217
MAPKAPK5 0.0383117845
C2CD2 0.0402856280
WDR7 -0.0208450395
SUPV3L1 -0.0134663710
THAP11 -0.0305872650
RFNG -0.0504759670
APBB2 0.0288108216
HOXA10 0.0128787805
COG7 -0.0476206770
TICAM1 0.1201310820
GDPD5 0.0793159285
PLCB3 0.0333728450
SPDEF 0.0423500932
FCHO1 -0.0118323900
NENF 0.0141299525
SOX2 -0.0611985997
HOXA5 0.0788659540
TMEM110 0.0313531060
NFKBIB -0.0021516990
ARID4B 0.0259249195
RALA 0.0206823150
ARPP19 0.0093898023
CCNB1 0.0680331705
RBM34 -0.0290578820
DNM1 -0.1018115985
WDR61 0.0028901950
AKAP8L 0.0370965048
IGHMBP2 0.0132725483
PPP1R13B 0.0162129180
CCL2 0.1424147770
NGRN 0.0036667283
ADI1 0.0074927940
RAB31 -0.0780890207
TMEM50A 0.0210497625
YKT6 0.0159397940
UBE2J1 0.0731200617
EVL 0.0074057920
BACE2 -0.0245869113
PIH1D1 -0.0037112750
CAB39 0.0043392200
IARS2 0.0586633540
BAG3 -0.0359330670
LAP3 0.0353684010
STUB1 -0.0398094837
ENOPH1 0.0312823140
SQRDL -0.0533107540
MRPS2 0.0075857010
NUP85 0.0125252420
NUSAP1 0.0617493280
MRPS16 0.0217226125
NPDC1 -0.0484566490
UBR7 0.0221665760
TMEM2 -0.0259300750
ZNF395 0.0506821433
ADCK3 0.0122316590
ISOC1 0.1764540910
CCDC92 -0.0495760880
GOLT1B 0.0397577700
SCAND1 -0.0215070780
NR1H2 -0.0889810660
TSKU 0.0496492150
ZDHHC6 0.0052835320
TIMM9 0.0600677870
GMNN 0.0073228080
CRELD2 0.0206527410
NUDT9 0.0265541420
CDCA4 0.0547367810
CERK -0.0696747570
KCTD5 -0.0171017393
CD320 0.0753358300
DHDDS -0.0545451985
SUV39H1 -0.0061926660
VPS28 -0.0089665520
NARFL -0.0755056980
CHMP6 -0.0538229850
KIF20A 0.0737769920
HOOK2 0.0225532420
VAV3 0.0052280440
SLC35F2 0.0006165820
IGF2BP2 0.0289402380
FAM57A -0.0328129570
NOTCH1 0.0534230790
ANO10 -0.0043653940
FASTKD5 0.0275351460
LAGE3 -0.0140379190
AMDHD2 -0.1922636650
PRR15L 0.0347196440
FSD1 -0.1779230860
TIMM22 -0.0020847937
RBKS 0.0737755380
CHAC1 0.0236545150
MSRA -0.1316496870
ADAT1 -0.0718148460
FKBP14 0.0170483917
CHIC2 -0.0017746890
PRR7 0.0211565820
SPAG4 0.0658832550
MCOLN1 -0.0060871320
SLC2A6 0.1017468040
FBXL12 0.0026517195
SNX11 0.0182990100
ATG3 0.0222526545
FAIM 0.0785146920
GTPBP8 -0.0086561470
PECR -0.0065644375
FRS2 0.0047739027
BNIP3L 0.0021209925
GRWD1 0.0377533780
ABHD6 -0.0540747987
SIRT3 -0.0033130537
STAP2 0.0137236800
ACOT9 0.0332240610
YTHDF1 -0.0083579240
MICALL1 0.0310617985
FAM63A -0.0696536875
P4HTM -0.0077015290
SLC27A3 -0.1012534970
MACF1 -0.0296154260
NPEPL1 0.0172414015th <- subset(df, df$G3 > 0.1 | df$G3 < -0.1)
th G3
GNB5 0.1271500
PTGS2 0.1358661
EDN1 -0.1278628
EGFR -0.1007566
KCNK1 -0.1488073
SERPINE1 0.1047676
PTPRF 0.1314563
HK1 -0.1219286
PLP2 0.1206142
TOMM70A 0.1033180
UBE2L6 -0.1124652
MYBL2 0.1086395
ALDOC -0.2632687
TRAK2 0.1188727
MYC 0.4261564
LYN -0.1521439
PSMB10 -0.1004492
PCK2 0.1925205
CRYZ 0.1492747
LYPLA1 0.1457716
PTPRK -0.2782815
PTK2B -0.1000499
TLE1 -0.2104426
CDH3 -0.3558887
SOCS2 -0.1199872
PSMG1 0.1374730
LOXL1 0.1454032
FZD7 0.1659426
BUB1B 0.1017785
TCEA2 -0.1103101
PRKX -0.1260800
SLC5A6 0.1094041
FZD1 0.1762483
SNCA -0.2755467
ACD -0.1070586
ICAM3 -0.1171769
CBR3 -0.1874948
C5 -0.1664310
NOS3 0.2551925
KIF14 0.1121642
SYK 0.3033506
PDLIM1 0.1391876
PSMB8 0.2495461
CORO1A -0.1049920
VGLL4 -0.1245173
CHN1 -0.1051355
TICAM1 0.1201311
DNM1 -0.1018116
CCL2 0.1424148
ISOC1 0.1764541
AMDHD2 -0.1922637
FSD1 -0.1779231
MSRA -0.1316497
SLC2A6 0.1017468
SLC27A3 -0.1012535L1000_signature_data <- read.table(file = "matPH3_2_1_0.2_0.3_L1000_Batch2017_Regina_removed.txt", row.names = 1, header = TRUE)
head(L1000_signature_data) AARS ABCB6 ABCC5 ABCF1 ABCF3 ABHD4 ABHD6 ABL1 ACAA1 ACAT2 ACBD3 ACD ACLY ACOT9 ADAM10 ADAT1 ADCK3 ADH5 ADI1 ADO ADRB2 AGL AKAP8 AKAP8L AKR7A2
10-DEBC 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 0
AKT1 ALAS1 ALDH7A1 ALDOA ALDOC AMDHD2 ANKRD10 ANO10 ANXA7 APBB2 APOE APP APPBP2 ARFIP2 ARHGAP1 ARHGEF12 ARHGEF2 ARID4B ARID5B ARL4C ARNT2
10-DEBC -3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0
ARPP19 ASAH1 ASCC3 ATF1 ATF5 ATF6 ATG3 ATMIN ATP11B ATP1B1 ATP2C1 ATP5S ATP6V0B ATP6V1D AURKA AURKB AXIN1 BACE2 BAD BAG3 BAMBI BAX BCL2 BCL7B
10-DEBC 0 0 0 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 0 0 0 0 -3 0
BDH1 BECN1 BHLHE40 BID BIRC2 BIRC5 BLCAP BLMH BLVRA BMP4 BNIP3 BNIP3L BPHL BRCA1 BTK BUB1B BZW2 C2CD2 C2CD2L C5 CAB39 CALM3 CALU CAMSAP2
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
CANT1 CAPN1 CASC3 CASK CASP10 CASP2 CASP3 CASP7 CAST CAT CBLB CBR1 CBR3 CCDC85B CCDC86 CCDC92 CCL2 CCNA1 CCNA2 CCNB1 CCNB2 CCND1 CCND3 CCNE2
10-DEBC 0 0 -3 -3 0 0 0 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 0 0
CCNF CCNH CCP110 CD320 CD40 CD44 CD58 CDC20 CDC25A CDC25B CDC42 CDC45 CDCA4 CDH3 CDK1 CDK19 CDK2 CDK4 CDK5R1 CDK6 CDK7 CDKN1A CDKN1B CDKN2A
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 4 0 0 0 0 0 0 0
CEBPA CEBPD CEBPZ CENPE CEP57 CERK CETN3 CFLAR CGRRF1 CHAC1 CHEK1 CHEK2 CHERP CHIC2 CHMP4A CHMP6 CHN1 CIAPIN1 CIRBP CISD1 CLIC4 CLPX CLSTN1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 0 0 0
CLTB CLTC CNDP2 CNOT4 CNPY3 COASY COG2 COG4 COG7 COL1A1 COL4A1 COPB2 COPS7A CORO1A CPNE3 CPSF4 CREB1 CREG1 CRELD2 CRK CRKL CRTAP CRYZ CSK
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0
CSNK1A1 CSNK1E CSNK2A2 CSRP1 CTNNAL1 CTNND1 CTSD CTTN CXCL2 CXCR4 CYB561 CYCS CYTH1 DAG1 DAXX DCK DCTD DCUN1D4 DDB2 DDIT4 DDR1 DDX10 DDX42
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0
DECR1 DENND2D DERA DFFA DFFB DHDDS DHRS7 DHX29 DLD DMTF1 DNAJA3 DNAJB1 DNAJB2 DNAJB6 DNAJC15 DNM1 DNM1L DNMT1 DNMT3A DNTTIP2 DPH2 DRAP1 DSG2
10-DEBC 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 3 -3 0 0 0 0 0 -3 0
DUSP11 DUSP14 DUSP22 DUSP3 DUSP4 DUSP6 DYNLT3 DYRK3 E2F2 EAPP EBNA1BP2 EBP ECD ECH1 EDEM1 EDN1 EED EGF EGFR EGR1 EIF4EBP1 EIF4G1 EIF5 ELAC2
10-DEBC 3 0 0 0 0 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 0 0 0 -3
ELAVL1 ELOVL6 EML3 ENOPH1 ENOSF1 EPB41L2 EPHA3 EPHB2 EPN2 EPRS ERBB2 ERBB3 ETFB ETS1 ETV1 EVL EXOSC4 EXT1 EZH2 FAH FAIM FAM20B FAM57A FAM63A
10-DEBC 0 0 -3 0 0 -3 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 3 0 0 0
FAM69A FAS FASTKD5 FAT1 FBXL12 FBXO11 FBXO21 FBXO7 FCHO1 FDFT1 FEZ2 FGFR2 FGFR4 FHL2 FIS1 FKBP14 FKBP4 FOS FOSL1 FOXJ3 FOXO3 FOXO4 FPGS FRS2
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 0 0 0
FSD1 FUT1 FYN FZD1 FZD7 G3BP1 GAA GABPB1 GADD45A GADD45B GALE GAPDH GATA2 GATA3 GDPD5 GFOD1 GFPT1 GHR GLI2 GLOD4 GLRX GMNN GNA11 GNA15 GNAI1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 0
GNAI2 GNAS GNB5 GNPDA1 GOLT1B GPATCH8 GPC1 GRB10 GRB7 GRN GRWD1 GSTM2 GSTZ1 GTF2A2 GTF2E2 GTPBP8 H2AFV HADH HAT1 HDAC2 HDAC6 HDGFRP3 HEATR1
10-DEBC 0 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HEBP1 HERC6 HERPUD1 HES1 HIF1A HIST1H2BK HIST2H2BE HK1 HMG20B HMGA2 HMGCR HMGCS1 HMOX1 HN1L HOMER2 HOOK2 HOXA10 HOXA5 HPRT1 HS2ST1 HSD17B10
10-DEBC 0 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 0 0 0 3 0
HSD17B11 HSPA1A HSPA4 HSPA8 HSPB1 HSPD1 HTATSF1 HTRA1 HYOU1 IARS2 ICAM1 ICAM3 ICMT ID2 IDE IER3 IFNAR1 IFRD2 IGF1R IGF2BP2 IGF2R IGFBP3
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0
IGHMBP2 IKBKAP IKBKB IKBKE IKZF1 IL13RA1 IL1B IL4R ILK INPP1 INPP4B INSIG1 INTS3 IPO13 IQGAP1 ISOC1 ITFG1 ITGAE ITGB1BP1 ITGB5 JMJD6 JUN
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
KAT6A KAT6B KCNK1 KCTD5 KDELR2 KDM3A KDM5A KDM5B KEAP1 KIAA0100 KIAA0196 KIAA0355 KIAA0753 KIAA0907 KIAA1033 KIF14 KIF20A KIF2C KIF5C KIT
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 -4 0 0 -3 0 0 3
KLHDC2 KLHL21 KLHL9 KTN1 LAGE3 LAMA3 LAP3 LBR LGALS8 LGMN LIG1 LIPA LOXL1 LPAR2 LPGAT1 LRP10 LRPAP1 LRRC16A LRRC41 LSM5 LSM6 LSR LYN LYPLA1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 0 0 0 3 0 0 3
LYRM1 MACF1 MALT1 MAMLD1 MAN2B1 MAP2K5 MAP3K4 MAP4K4 MAP7 MAPK13 MAPK1IP1L MAPK9 MAPKAPK2 MAPKAPK3 MAPKAPK5 MAST2 MAT2A MBNL1 MBNL2 MBOAT7
10-DEBC 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 0 0 0 0 0 0
MBTPS1 MCM3 MCOLN1 ME2 MEF2C MELK MEST METRN MFSD10 MICALL1 MIF MKNK1 MLEC MLLT11 MMP1 MMP2 MNAT1 MOK MPZL1 MRPL12 MRPL19 MRPS16 MRPS2 MSH6
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MSRA MTA1 MTF2 MTFR1 MTHFD2 MUC1 MVP MYBL2 MYC MYCBP MYCBP2 MYL9 MYLK MYO10 NARFL NCAPD2 NCK1 NCK2 NCOA3 NENF NET1 NFATC3 NFATC4 NFE2L2 NFIL3
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 0 0 0 0
NFKB2 NFKBIA NFKBIB NFKBIE NGRN NIPSNAP1 NISCH NIT1 NMT1 NNT NOL3 NOLC1 NOS3 NOSIP NOTCH1 NPC1 NPDC1 NPEPL1 NPRL2 NR1H2 NR2F6 NR3C1 NRAS
10-DEBC 0 0 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
NRIP1 NSDHL NT5DC2 NUCB2 NUDCD3 NUDT9 NUP133 NUP62 NUP85 NUP88 NUP93 NUSAP1 NVL ORC1 OXA1L OXCT1 OXSR1 P4HA2 P4HTM PACSIN3 PAF1 PAFAH1B1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
PAFAH1B3 PAICS PAK1 PAK4 PAK6 PAN2 PAPD7 PARP1 PARP2 PAX8 PCBD1 PCCB PCK2 PCM1 PCMT1 PCNA PDGFA PDHX PDIA5 PDLIM1 PDS5A PECR PEX11A PFKL
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 0 0 0 0 0
PGAM1 PGM1 PGRMC1 PHGDH PHKA1 PHKB PHKG2 PIGB PIH1D1 PIK3C2B PIK3C3 PIK3CA PIK3R3 PIK3R4 PIN1 PIP4K2B PKIG PLA2G15 PLA2G4A PLCB3 PLEKHJ1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
PLEKHM1 PLK1 PLOD3 PLP2 PLS1 PLSCR1 PLSCR3 PMAIP1 PMM2 PNKP PNP POLB POLD4 POLE2 POLG2 POLR1C POLR2I POLR2K POP4 PPARD PPARG PPIC PPIE PPOX
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 3 0 0 0 3 0 0
PPP1R13B PPP2R3C PPP2R5A PPP2R5E PRAF2 PRCP PRKACA PRKAG2 PRKCD PRKCH PRKCQ PRKX PROS1 PRPF4 PRR15L PRR7 PRSS23 PRUNE PSIP1 PSMB10 PSMB8
10-DEBC 0 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 0 0 0 0 0
PSMD10 PSMD2 PSMD4 PSMD9 PSME1 PSME2 PSMF1 PSMG1 PSRC1 PTGS2 PTK2 PTK2B PTPN1 PTPN12 PTPN6 PTPRC PTPRF PTPRK PUF60 PWP1 PXMP2 PXN PYCR1 PYGL
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0
RAB11FIP2 RAB21 RAB27A RAB31 RAB4A RAC2 RAD51C RAD9A RAE1 RAI14 RALA RALB RALGDS RAP1GAP RASA1 RB1 RBKS RBM15B RBM34 RBM6 REEP5 RELB RFC2
10-DEBC -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 0 -5 0 0 0
RFC5 RFNG RFX5 RGS2 RHEB RHOA RNF167 RNH1 RNMT RNPS1 RPA1 RPA2 RPA3 RPIA RPL39L RPN1 RPP38 RPS5 RPS6 RPS6KA1 RRAGA RRP12 RRP1B RRP8 RRS1 RSU1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
RTN2 RUVBL1 S100A13 S100A4 SACM1L SATB1 SCAND1 SCARB1 SCCPDH SCP2 SCRN1 SCYL3 SDHB SENP6 SERPINE1 SESN1 SFN SGCB SH3BP5 SHB SHC1 SIRT3 SKIV2L
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3
SKP1 SLC11A2 SLC1A4 SLC25A13 SLC25A14 SLC25A4 SLC25A46 SLC27A3 SLC2A6 SLC35A1 SLC35A3 SLC35B1 SLC35F2 SLC37A4 SLC5A6 SMAD3 SMARCA4 SMARCC1
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0
SMARCD2 SMC1A SMC3 SMC4 SMNDC1 SNAP25 SNCA SNX11 SNX13 SNX6 SNX7 SOCS2 SORBS3 SOX2 SOX4 SPAG4 SPAG7 SPDEF SPEN SPP1 SPR SPRED2 SPTAN1 SPTLC2
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -4 0 0 0 0 0
SQRDL SQSTM1 SRC SSBP2 ST3GAL5 ST6GALNAC2 ST7 STAMBP STAP2 STAT1 STAT3 STAT5B STK10 STK25 STMN1 STUB1 STX1A STX4 STXBP1 STXBP2 SUPV3L1
10-DEBC 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -3 0 0 0 0
SUV39H1 SUZ12 SYK SYNE2 SYNGR3 SYPL1 TARBP1 TATDN2 TBC1D9B TBP TBPL1 TBX2 TBXA2R TCEA2 TCEAL4 TCERG1 TCFL5 TCTA TCTN1 TERF2IP TERT TES TESK1
10-DEBC 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0
TEX10 TFAP2A TFDP1 TGFB3 TGFBR2 THAP11 TIAM1 TICAM1 TIMELESS TIMM17B TIMM22 TIMM9 TIMP2 TIPARP TJP1 TLE1 TLK2 TLR4 TM9SF2 TM9SF3 TMCO1 TMED10
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TMEM109 TMEM110 TMEM2 TMEM5 TMEM50A TMEM97 TNFRSF21 TNIP1 TOMM34 TOMM70A TOP2A TOPBP1 TOR1A TP53 TP53BP1 TP53BP2 TPD52L2 TPM1 TRAK2 TRAM2
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TRAP1 TRAPPC3 TRAPPC6A TRIB1 TRIB3 TRIM13 TRIM2 TSC22D3 TSEN2 TSKU TSPAN3 TSPAN4 TSPAN6 TSTA3 TUBB6 TWF2 TXLNA TXNDC9 TXNL4B TXNRD1 UBE2A
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 -4 0
UBE2C UBE2J1 UBE2L6 UBE3B UBE3C UBQLN2 UBR7 UFM1 UGDH USP1 USP14 USP22 USP6NL USP7 UTP14A VAPB VAT1 VAV3 VDAC1 VGLL4 VPS28 VPS72 WASF3 WDR61
10-DEBC 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0
WDR7 WDTC1 WFS1 WIPF2 WRB XBP1 XPNPEP1 XPO7 YKT6 YME1L1 YTHDF1 ZDHHC6 ZFP36 ZMIZ1 ZMYM2 ZNF131 ZNF274 ZNF318 ZNF395 ZNF451 ZNF586 ZNF589 ZW10
10-DEBC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[ reached 'max' / getOption("max.print") -- omitted 5 rows ]target_compound <- "triptolide"
compound_sig <- as.data.frame(t(subset(L1000_signature_data, rownames(L1000_signature_data) == target_compound)))
compound_sig <- subset(compound_sig, rownames(compound_sig) %in% rownames(th))
data <- compound_sig$triptolide
names(data) <- rownames(compound_sig)
data ACD ALDOC AMDHD2 BUB1B C5 CBR3 CCL2 CDH3 CHN1 CORO1A CRYZ DNM1 EDN1 EGFR FSD1 FZD1
5 5 4 7 7 -3 3 5 4 4 -4 4 7 -6 7 7
FZD7 GNB5 HK1 ICAM3 ISOC1 KCNK1 KIF14 LOXL1 LYN LYPLA1 MSRA MYBL2 MYC NOS3 PCK2 PDLIM1
-6 7 -5 -5 5 -4 -6 3 6 -5 5 7 -5 5 6 4
PLP2 PRKX PSMB10 PSMB8 PSMG1 PTGS2 PTK2B PTPRF PTPRK SERPINE1 SLC27A3 SLC2A6 SLC5A6 SNCA SOCS2 SYK
7 7 4 -3 -7 5 7 7 6 6 6 -3 3 5 7 5
TCEA2 TICAM1 TLE1 TOMM70A TRAK2 UBE2L6 VGLL4
7 3 -6 -7 -7 6 -5 barplot(data, horiz = TRUE, col = "red")
pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)
pdf(file = "triptolide_subset_sig_heatmap.pdf")
pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)
dev.off()pdf
3
Now, can we just make a barplot of the spearman correlations?
data <- as.numeric(c(SC.G3, SC.G4, SC.WNT, SC.SHH))
names(data) <- c("G3", "G4", "WNT", "SHH")
data G3 G4 WNT SHH
-0.16904001 0.05244407 0.02907768 0.05397576 barplot(data, horiz = TRUE, col = "red")
pdf(file = "triptolide_spearmancorrelation_barplot.pdf")barplot(data, horiz = TRUE, col = "red")
dev.off()png
2 
Now, it would be pretty cool to cluster the data on this signature and see how it looks…
head(dat)
G4 G4.1 G4.2 G4.3 G4.4 G4.5 G4.6 G4.7 G4.8 G4.9 G4.10 G4.11 G4.12 G4.13 G4.14 G4.15
1 7.595940 7.806655 7.401414 7.603100 7.996856 7.825205 7.683266 7.457205 7.562213 7.349231 7.692980 6.847049 6.988782 7.347686 7.491087 7.481837
2 6.144400 6.191544 5.907811 6.052795 6.883360 6.283014 5.882486 6.577583 5.841223 6.801283 6.385026 6.321308 6.137943 6.116995 6.906354 6.583686
4 5.670915 5.621487 5.978379 5.599533 5.769882 5.278115 5.732694 5.846439 5.827768 5.992464 5.660527 5.930387 5.950121 5.687315 6.205769 5.967428
14 6.035960 5.816218 6.104124 5.679490 6.089272 5.871273 5.993961 6.450154 6.602588 5.420535 6.050676 5.884714 5.613128 6.012981 5.631928 6.933715
156 3.384390 3.044523 3.629660 3.077312 3.653252 3.126760 3.025291 3.091043 3.711130 3.363842 3.660994 3.161247 3.871201 4.003690 3.779634 4.096010
263 4.891101 3.517498 3.303217 3.462606 3.508556 3.624341 4.385770 4.837075 3.325036 3.380995 3.558201 3.468856 4.508659 3.246491 4.514151 4.326778
G4.16 G4.17 G4.18 G4.19 G4.20 G4.21 G4.22 G4.23 G4.24 G4.25 G4.26 G4.27 G4.28 G4.29 G4.30 G4.31
1 7.670195 7.220520 7.658086 7.767983 6.940416 7.127614 6.386037 7.178317 7.387895 7.024382 7.156177 7.432957 6.742055 7.073693 7.285918 6.946303
2 6.274951 6.270232 6.959778 6.529857 6.283947 6.006599 6.608406 5.874931 6.296741 6.148041 6.606785 5.929855 6.291013 7.048820 6.531606 6.224955
4 5.742362 5.824524 5.388158 6.076265 6.026107 5.838604 5.771130 5.280153 5.179534 5.875493 5.623295 5.231109 5.210578 5.786283 5.412539 5.220356
14 6.013471 5.510198 5.909169 5.633718 5.349486 5.896329 5.532203 5.838314 6.545781 6.066804 5.773309 5.889155 5.719328 5.975335 5.530222 6.104347
156 3.708682 3.157000 3.742420 3.624341 3.914021 3.487375 3.686376 3.841601 3.186353 3.931826 3.797734 3.493473 4.259859 3.104587 3.747148 3.095578
263 3.505557 4.197202 4.027136 4.432006 3.394508 3.122365 3.698830 3.602777 3.627004 4.403054 3.152736 3.173878 3.310543 3.758872 3.292126 3.449988
G4.32 G4.33 G4.34 G4.35 G4.36 G4.37 G4.38 G3 G3.1 G3.2 G3.3 G3.4 G3.5 G3.6 G3.7 G3.8
1 7.805026 7.751303 7.649788 7.330798 7.500640 7.667673 7.757735 7.792349 8.260027 7.332892 7.128977 6.899421 6.170656 7.302496 7.727711 7.287560
2 6.617671 6.372637 6.606785 5.766757 6.388730 6.606110 6.893149 6.579529 7.080868 6.642747 6.012002 6.596873 6.690097 6.358189 6.204356 6.734591
4 5.660875 5.980151 5.861640 5.938591 5.984188 5.436774 6.090857 6.212406 6.282827 6.110358 5.918625 6.018593 5.894954 5.746522 6.061457 5.905362
14 5.792709 6.765039 6.683861 6.286184 5.593596 5.412092 6.150390 6.256134 6.440149 5.957132 6.131661 5.810243 7.059016 5.754158 6.413131 7.300203
156 3.735286 3.446808 3.157000 3.226844 3.100092 3.034953 3.173878 3.716008 3.770459 3.449988 3.139832 3.624341 3.535145 3.015535 3.605498 3.555348
263 3.718438 3.182212 3.325036 3.258096 3.363842 3.265759 3.538057 3.194583 3.317816 3.397858 3.178054 3.972177 3.190476 3.374169 3.992681 4.104295
G3.9 G3.10 G3.11 G3.12 G3.13 G3.14 G3.15 WNT WNT.1 WNT.2 WNT.3 WNT.4 WNT.5 WNT.6 WNT.7 SHH
1 6.780603 7.560757 6.719979 7.536524 6.942350 7.408894 6.756235 7.600802 7.725507 6.760878 7.165107 6.799502 7.647977 6.919091 6.641443 7.545496
2 6.830982 6.795929 7.313420 6.337003 6.025624 6.564560 6.335409 5.974064 6.624198 6.735305 6.163946 6.448573 6.202940 6.602316 6.553648 6.178773
4 5.780435 5.378514 5.666773 5.862210 5.369708 5.897429 5.580861 5.785977 5.922650 5.800607 5.441985 5.772686 5.318610 5.808143 5.411200 6.218002
14 7.105622 5.085124 6.742763 6.637520 5.778890 5.557214 5.903998 6.738745 6.490875 6.491330 6.100095 6.589751 5.998937 6.041920 5.840641 6.991361
156 4.041296 3.284664 3.049273 3.058707 3.117950 4.007333 4.067316 3.117950 3.254243 3.756538 4.019980 3.832980 3.879500 3.314186 3.310543 3.901973
263 3.906005 3.484312 3.222868 3.238678 3.856510 3.770459 3.511545 3.380995 3.250375 3.242592 3.280911 3.131137 3.325036 3.126760 3.332205 3.610918
SHH.1 SHH.2 SHH.3 SHH.4 SHH.5 SHH.6 SHH.7 SHH.8 SHH.9 Gene.Symbol
1 7.937874 7.673595 6.877605 6.945340 7.776745 7.462502 7.460433 7.466914 7.750744 DDR1
2 6.507725 6.100991 6.377067 6.315358 6.776963 6.173369 6.482343 6.058188 6.541607 RFC2
4 5.592478 5.796361 6.023205 5.615680 5.797880 5.792709 5.859931 5.993961 6.115450 PAX8
14 6.294343 6.667593 7.128335 6.386711 6.940416 6.477126 5.790877 6.324000 6.066108 SCARB1
156 3.629660 3.072693 3.303217 3.895894 3.374169 3.921973 3.929863 3.740048 3.788725 PTPRC
263 3.292126 3.182212 3.629660 3.475067 3.269569 3.242592 4.266896 3.242592 3.437208 JMJD6dat2 <- dat %>% group_by(Gene.Symbol) %>% mutate_each(funs(mean), -(0)) %>% distinct
head(dat2)rownames(dat2) <- dat2$Gene.SymbolSetting row names on a tibble is deprecated.# MedulloSigs <- dat2
# rm(dat)
# rm(dat2)
head(dat2)names(cmpd_ordered) [1] "ABCF1" "ABCF3" "ABHD6" "ABL1" "ACAA1" "ACBD3" "ACD" "ACLY" "ACOT9" "ADAM10" "ADAT1"
[12] "ADCK3" "ADH5" "ADI1" "ADO" "AGL" "AKAP8" "AKAP8L" "ALAS1" "ALDH7A1" "ALDOC" "AMDHD2"
[23] "ANO10" "ANXA7" "APBB2" "APOE" "APPBP2" "ARFIP2" "ARHGAP1" "ARHGEF12" "ARHGEF2" "ARID4B" "ARID5B"
[34] "ARL4C" "ARNT2" "ARPP19" "ASAH1" "ASCC3" "ATF1" "ATF5" "ATG3" "ATMIN" "ATP11B" "ATP1B1"
[45] "ATP2C1" "ATP5S" "ATP6V0B" "AURKA" "AURKB" "BACE2" "BAD" "BAG3" "BAMBI" "BAX" "BCL2"
[56] "BCL7B" "BHLHE40" "BID" "BIRC2" "BLCAP" "BLMH" "BLVRA" "BMP4" "BNIP3" "BNIP3L" "BPHL"
[67] "BRCA1" "BTK" "BUB1B" "C2CD2" "C2CD2L" "C5" "CAB39" "CALM3" "CALU" "CAMSAP2" "CANT1"
[78] "CASC3" "CASK" "CASP10" "CASP2" "CASP3" "CASP7" "CAST" "CAT" "CBLB" "CBR1" "CBR3"
[89] "CCDC92" "CCL2" "CCNA1" "CCNA2" "CCNB1" "CCNB2" "CCND3" "CCNF" "CCNH" "CCP110" "CD320"
[100] "CD40" "CD44" "CDC20" "CDC25A" "CDC25B" "CDC42" "CDC45" "CDCA4" "CDH3" "CDK1" "CDK19"
[111] "CDK4" "CDK5R1" "CDK7" "CDKN1B" "CDKN2A" "CEBPD" "CEBPZ" "CENPE" "CERK" "CGRRF1" "CHAC1"
[122] "CHEK1" "CHEK2" "CHERP" "CHIC2" "CHMP6" "CHN1" "CLIC4" "CLPX" "CLTB" "CLTC" "CNDP2"
[133] "CNOT4" "CNPY3" "COG4" "COG7" "COL1A1" "COPB2" "COPS7A" "CORO1A" "CPNE3" "CPSF4" "CREG1"
[144] "CRELD2" "CRK" "CRKL" "CRTAP" "CRYZ" "CSK" "CSNK1A1" "CSNK1E" "CSNK2A2" "CSRP1" "CTNND1"
[155] "CTSD" "CXCR4" "CYCS" "CYTH1" "DAXX" "DCK" "DCUN1D4" "DDB2" "DDR1" "DDX10" "DDX42"
[166] "DECR1" "DFFA" "DFFB" "DHDDS" "DHRS7" "DHX29" "DLD" "DMTF1" "DNAJA3" "DNAJB1" "DNAJB6"
[177] "DNM1" "DNMT1" "DNTTIP2" "DPH2" "DUSP11" "DUSP14" "DYRK3" "E2F2" "EAPP" "EBNA1BP2" "EBP"
[188] "ECD" "ECH1" "EDEM1" "EDN1" "EED" "EGF" "EGFR" "EIF4G1" "EIF5" "ELAC2" "ELOVL6"
[199] "EML3" "ENOPH1" "EPHA3" "EPHB2" "EPN2" "EPRS" "ERBB2" "ETS1" "EVL" "EXT1" "EZH2"
[210] "FAH" "FAIM" "FAM20B" "FAM57A" "FAM63A" "FAM69A" "FAS" "FASTKD5" "FBXL12" "FBXO11" "FBXO21"
[221] "FBXO7" "FCHO1" "FDFT1" "FEZ2" "FGFR2" "FGFR4" "FHL2" "FKBP14" "FKBP4" "FOS" "FOSL1"
[232] "FOXJ3" "FOXO3" "FOXO4" "FRS2" "FSD1" "FUT1" "FZD1" "FZD7" "G3BP1" "GAA" "GABPB1"
[243] "GADD45A" "GADD45B" "GALE" "GAPDH" "GDPD5" "GFOD1" "GLI2" "GLOD4" "GLRX" "GMNN" "GNA11"
[254] "GNA15" "GNAS" "GNB5" "GOLT1B" "GPATCH8" "GPC1" "GRB7" "GRN" "GRWD1" "GSTM2" "GSTZ1"
[265] "GTF2A2" "GTF2E2" "GTPBP8" "H2AFV" "HAT1" "HDAC2" "HEATR1" "HERC6" "HIF1A" "HIST1H2BK" "HIST2H2BE"
[276] "HK1" "HMGCR" "HMGCS1" "HMOX1" "HN1L" "HOMER2" "HOOK2" "HOXA10" "HOXA5" "HS2ST1" "HSPA1A"
[287] "HSPA4" "HSPA8" "HSPD1" "HTATSF1" "HTRA1" "HYOU1" "IARS2" "ICAM1" "ICAM3" "ID2" "IDE"
[298] "IER3" "IFNAR1" "IFRD2" "IGF1R" "IGF2BP2" "IGF2R" "IGFBP3" "IGHMBP2" "IKBKAP" "IKBKB" "IKBKE"
[309] "IKZF1" "IL13RA1" "IL1B" "IL4R" "INPP1" "INPP4B" "INSIG1" "INTS3" "IPO13" "IQGAP1" "ISOC1"
[320] "ITFG1" "ITGAE" "ITGB5" "JMJD6" "JUN" "KAT6A" "KCNK1" "KCTD5" "KDM3A" "KDM5A" "KDM5B"
[331] "KIAA0196" "KIAA0355" "KIAA0753" "KIAA0907" "KIAA1033" "KIF14" "KIF20A" "KIF2C" "KIF5C" "KIT" "LAGE3"
[342] "LAP3" "LBR" "LGALS8" "LGMN" "LOXL1" "LPAR2" "LPGAT1" "LRPAP1" "LSM5" "LSM6" "LSR"
[353] "LYN" "LYPLA1" "MACF1" "MAN2B1" "MAP2K5" "MAP3K4" "MAP4K4" "MAPK1IP1L" "MAPK9" "MAPKAPK2" "MAPKAPK3"
[364] "MAPKAPK5" "MAT2A" "MBNL1" "MBNL2" "MBTPS1" "MCM3" "MCOLN1" "MELK" "MEST" "MICALL1" "MKNK1"
[375] "MMP1" "MMP2" "MNAT1" "MPZL1" "MRPL12" "MRPL19" "MRPS16" "MRPS2" "MSH6" "MSRA" "MTA1"
[386] "MTF2" "MTFR1" "MTHFD2" "MVP" "MYBL2" "MYC" "MYCBP2" "MYL9" "MYO10" "NARFL" "NCAPD2"
[397] "NCK1" "NCK2" "NCOA3" "NENF" "NET1" "NFATC4" "NFE2L2" "NFKB2" "NFKBIA" "NFKBIB" "NFKBIE"
[408] "NGRN" "NISCH" "NIT1" "NOL3" "NOLC1" "NOS3" "NOTCH1" "NPC1" "NPDC1" "NPEPL1" "NPRL2"
[419] "NR1H2" "NR2F6" "NRIP1" "NSDHL" "NT5DC2" "NUCB2" "NUDCD3" "NUDT9" "NUP62" "NUP85" "NUP88"
[430] "NUSAP1" "NVL" "ORC1" "OXA1L" "OXCT1" "OXSR1" "P4HTM" "PAF1" "PAFAH1B1" "PAICS" "PAPD7"
[441] "PARP2" "PAX8" "PCCB" "PCK2" "PCM1" "PCMT1" "PCNA" "PDGFA" "PDHX" "PDLIM1" "PDS5A"
[452] "PECR" "PFKL" "PGM1" "PHKA1" "PHKB" "PHKG2" "PIH1D1" "PIK3C2B" "PIK3CA" "PIK3R3" "PIK3R4"
[463] "PIP4K2B" "PLA2G4A" "PLCB3" "PLEKHM1" "PLK1" "PLOD3" "PLP2" "PLS1" "PMAIP1" "PMM2" "PNP"
[474] "POLD4" "POLE2" "POLG2" "POLR1C" "POLR2K" "POP4" "PPARD" "PPOX" "PPP1R13B" "PPP2R3C" "PPP2R5E"
[485] "PRCP" "PRKACA" "PRKCQ" "PRKX" "PROS1" "PRPF4" "PRR15L" "PRR7" "PRSS23" "PRUNE" "PSIP1"
[496] "PSMB10" "PSMB8" "PSMD10" "PSMD2" "PSMD4" "PSMD9" "PSMF1" "PSMG1" "PSRC1" "PTGS2" "PTK2"
[507] "PTK2B" "PTPN1" "PTPN12" "PTPRC" "PTPRF" "PTPRK" "PUF60" "PWP1" "PXN" "RAB21" "RAB27A"
[518] "RAB31" "RAB4A" "RAC2" "RAD51C" "RAD9A" "RAE1" "RAI14" "RALA" "RALB" "RAP1GAP" "RASA1"
[529] "RBKS" "RBM15B" "RBM34" "RBM6" "RFNG" "RFX5" "RGS2" "RHEB" "RNH1" "RNMT" "RNPS1"
[540] "RPA2" "RPA3" "RPL39L" "RPP38" "RPS5" "RPS6" "RRAGA" "RRP12" "RRP1B" "RRP8" "RSU1"
[551] "RTN2" "RUVBL1" "SACM1L" "SCAND1" "SCARB1" "SCCPDH" "SCP2" "SCYL3" "SDHB" "SENP6" "SERPINE1"
[562] "SFN" "SGCB" "SHB" "SHC1" "SIRT3" "SLC11A2" "SLC25A13" "SLC25A46" "SLC27A3" "SLC2A6" "SLC35A3"
[573] "SLC35B1" "SLC35F2" "SLC37A4" "SLC5A6" "SMAD3" "SMARCA4" "SMARCC1" "SMC3" "SMC4" "SMNDC1" "SNAP25"
[584] "SNCA" "SNX11" "SNX13" "SNX7" "SOCS2" "SOX2" "SOX4" "SPAG4" "SPAG7" "SPDEF" "SPEN"
[595] "SPR" "SPRED2" "SPTAN1" "SPTLC2" "SQRDL" "SQSTM1" "SRC" "SSBP2" "ST3GAL5" "ST6GALNAC2" "ST7"
[606] "STAMBP" "STAP2" "STAT5B" "STK10" "STUB1" "STX4" "STXBP1" "STXBP2" "SUPV3L1" "SUV39H1" "SUZ12"
[617] "SYK" "SYNE2" "SYPL1" "TARBP1" "TATDN2" "TBP" "TBPL1" "TBX2" "TBXA2R" "TCEA2" "TCERG1"
[628] "TCTA" "TCTN1" "TERF2IP" "TERT" "TES" "TESK1" "TFAP2A" "TGFB3" "TGFBR2" "THAP11" "TICAM1"
[639] "TIMELESS" "TIMM17B" "TIMM22" "TIMM9" "TIMP2" "TIPARP" "TJP1" "TLE1" "TLR4" "TM9SF2" "TMED10"
[650] "TMEM110" "TMEM2" "TMEM5" "TMEM50A" "TMEM97" "TOMM70A" "TOP2A" "TOR1A" "TP53BP1" "TP53BP2" "TPD52L2"
[661] "TPM1" "TRAK2" "TRAM2" "TRAP1" "TRAPPC3" "TRAPPC6A" "TRIB3" "TRIM13" "TRIM2" "TSEN2" "TSKU"
[672] "TUBB6" "TWF2" "TXLNA" "TXNDC9" "TXNRD1" "UBE2C" "UBE2J1" "UBE2L6" "UBE3B" "UBR7" "USP1"
[683] "USP14" "USP22" "USP6NL" "USP7" "VAT1" "VAV3" "VDAC1" "VGLL4" "VPS28" "VPS72" "WASF3"
[694] "WDR61" "WDR7" "WIPF2" "WRB" "XBP1" "XPNPEP1" "XPO7" "YKT6" "YTHDF1" "ZDHHC6" "ZFP36"
[705] "ZMYM2" "ZNF131" "ZNF395" "ZNF589" "ZW10" dat3 <- subset(dat2, rownames(dat2) %in% rownames(compound_sig))
dat4<-dat3
dat4$Gene.Symbol <- NULL
rownames(dat4) <- dat3$Gene.SymbolSetting row names on a tibble is deprecated.# rownames(dat3) <- dat3$Gene.Symbol
# dat3$Gene.Symbol <- NULL
pheatmap::pheatmap(dat4, scale = "row")
# How can we annotate this real quick.
g <- as.data.frame(colnames(dat4))
g colnames(dat4)
1 G4
2 G4.1
3 G4.2
4 G4.3
5 G4.4
6 G4.5
7 G4.6
8 G4.7
9 G4.8
10 G4.9
11 G4.10
12 G4.11
13 G4.12
14 G4.13
15 G4.14
16 G4.15
17 G4.16
18 G4.17
19 G4.18
20 G4.19
21 G4.20
22 G4.21
23 G4.22
24 G4.23
25 G4.24
26 G4.25
27 G4.26
28 G4.27
29 G4.28
30 G4.29
31 G4.30
32 G4.31
33 G4.32
34 G4.33
35 G4.34
36 G4.35
37 G4.36
38 G4.37
39 G4.38
40 G3
41 G3.1
42 G3.2
43 G3.3
44 G3.4
45 G3.5
46 G3.6
47 G3.7
48 G3.8
49 G3.9
50 G3.10
51 G3.11
52 G3.12
53 G3.13
54 G3.14
55 G3.15
56 WNT
57 WNT.1
58 WNT.2
59 WNT.3
60 WNT.4
61 WNT.5
62 WNT.6
63 WNT.7
64 SHH
65 SHH.1
66 SHH.2
67 SHH.3
68 SHH.4
69 SHH.5
70 SHH.6
71 SHH.7
72 SHH.8
73 SHH.9for (i in 1:length(g$`colnames(dat4)`)){
g$type[i] <- unlist(strsplit(as.character(g$`colnames(dat4)`[i]), split = ".", fixed = TRUE))[[1]]
}
g colnames(dat4) type
1 G4 G4
2 G4.1 G4
3 G4.2 G4
4 G4.3 G4
5 G4.4 G4
6 G4.5 G4
7 G4.6 G4
8 G4.7 G4
9 G4.8 G4
10 G4.9 G4
11 G4.10 G4
12 G4.11 G4
13 G4.12 G4
14 G4.13 G4
15 G4.14 G4
16 G4.15 G4
17 G4.16 G4
18 G4.17 G4
19 G4.18 G4
20 G4.19 G4
21 G4.20 G4
22 G4.21 G4
23 G4.22 G4
24 G4.23 G4
25 G4.24 G4
26 G4.25 G4
27 G4.26 G4
28 G4.27 G4
29 G4.28 G4
30 G4.29 G4
31 G4.30 G4
32 G4.31 G4
33 G4.32 G4
34 G4.33 G4
35 G4.34 G4
36 G4.35 G4
37 G4.36 G4
38 G4.37 G4
39 G4.38 G4
40 G3 G3
41 G3.1 G3
42 G3.2 G3
43 G3.3 G3
44 G3.4 G3
45 G3.5 G3
46 G3.6 G3
47 G3.7 G3
48 G3.8 G3
49 G3.9 G3
50 G3.10 G3
51 G3.11 G3
52 G3.12 G3
53 G3.13 G3
54 G3.14 G3
55 G3.15 G3
56 WNT WNT
57 WNT.1 WNT
58 WNT.2 WNT
59 WNT.3 WNT
60 WNT.4 WNT
61 WNT.5 WNT
62 WNT.6 WNT
63 WNT.7 WNT
64 SHH SHH
65 SHH.1 SHH
66 SHH.2 SHH
67 SHH.3 SHH
68 SHH.4 SHH
69 SHH.5 SHH
70 SHH.6 SHH
71 SHH.7 SHH
72 SHH.8 SHH
73 SHH.9 SHHe <- g
rownames(e) <- g$`colnames(dat4)`
e colnames(dat4) type
G4 G4 G4
G4.1 G4.1 G4
G4.2 G4.2 G4
G4.3 G4.3 G4
G4.4 G4.4 G4
G4.5 G4.5 G4
G4.6 G4.6 G4
G4.7 G4.7 G4
G4.8 G4.8 G4
G4.9 G4.9 G4
G4.10 G4.10 G4
G4.11 G4.11 G4
G4.12 G4.12 G4
G4.13 G4.13 G4
G4.14 G4.14 G4
G4.15 G4.15 G4
G4.16 G4.16 G4
G4.17 G4.17 G4
G4.18 G4.18 G4
G4.19 G4.19 G4
G4.20 G4.20 G4
G4.21 G4.21 G4
G4.22 G4.22 G4
G4.23 G4.23 G4
G4.24 G4.24 G4
G4.25 G4.25 G4
G4.26 G4.26 G4
G4.27 G4.27 G4
G4.28 G4.28 G4
G4.29 G4.29 G4
G4.30 G4.30 G4
G4.31 G4.31 G4
G4.32 G4.32 G4
G4.33 G4.33 G4
G4.34 G4.34 G4
G4.35 G4.35 G4
G4.36 G4.36 G4
G4.37 G4.37 G4
G4.38 G4.38 G4
G3 G3 G3
G3.1 G3.1 G3
G3.2 G3.2 G3
G3.3 G3.3 G3
G3.4 G3.4 G3
G3.5 G3.5 G3
G3.6 G3.6 G3
G3.7 G3.7 G3
G3.8 G3.8 G3
G3.9 G3.9 G3
G3.10 G3.10 G3
G3.11 G3.11 G3
G3.12 G3.12 G3
G3.13 G3.13 G3
G3.14 G3.14 G3
G3.15 G3.15 G3
WNT WNT WNT
WNT.1 WNT.1 WNT
WNT.2 WNT.2 WNT
WNT.3 WNT.3 WNT
WNT.4 WNT.4 WNT
WNT.5 WNT.5 WNT
WNT.6 WNT.6 WNT
WNT.7 WNT.7 WNT
SHH SHH SHH
SHH.1 SHH.1 SHH
SHH.2 SHH.2 SHH
SHH.3 SHH.3 SHH
SHH.4 SHH.4 SHH
SHH.5 SHH.5 SHH
SHH.6 SHH.6 SHH
SHH.7 SHH.7 SHH
SHH.8 SHH.8 SHH
SHH.9 SHH.9 SHHe$`colnames(dat4)` <- NULL
pheatmap::pheatmap(dat4, scale = "row", annotation_col = e)
pdf(file = "triptolide_mb_clusteringHeatmap.pdf")
pheatmap::pheatmap(dat4, scale = "row", annotation_col = e)
dev.off()pdf
3
---
title: "Obtain and Plot L1000 Signatures"
output: html_notebook
---

```{r}
L1000_signature_data <- read.table(file = "matPH3_2_1_0.2_0.3_L1000_Batch2017_Regina_removed.txt", row.names = 1, header = TRUE)

head(L1000_signature_data)

target_compound <- "triptolide"

compound_sig <- as.data.frame(t(subset(L1000_signature_data, rownames(L1000_signature_data) == target_compound)))
compound_sig <- subset(compound_sig, compound_sig$triptolide != 0)

data <- compound_sig$triptolide
names(data) <- rownames(compound_sig)
data

barplot(data, horiz = TRUE, col = "red")

pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)

pdf(file = "triptolide_sig_heatmap.pdf")
pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)
dev.off()
```

# So now subset this signature for genes within different medulloblastoma disease signatures. A good way to pick which one is ideal is to find which one this drug reverses the disease signature most of. 

So let's load in the medulloblastoma disease signature data from Anna. 
- This is a microarray dataset, so some genes have multiple probes. These probes are labeled for specificity, but for this purpose we will just average duplicate rows, so each gene's reported fold-change is representative of all probes for each gene. 

First, we should subset columns that are averagable.. ie. numeric
So Fold-change.

Then we will avverage the fold changes within each gene, and use that to calculate signature overlap with compound response signatures. 

```{r}
library(dplyr)
MedulloSigs <- read.csv(file = "MedulloSigs.csv", skip = 1, header = TRUE)
head(MedulloSigs)

myvars <- c("Gene.Symbol", "Log2FC_G4", "Log2FC_G3", "Log2FC_WNT", "Log2FC_SHH")
dat <- MedulloSigs[myvars]

myvars2 <- c("Log2FC_G4", "Log2FC_G3", "Log2FC_WNT", "Log2FC_SHH")
dat2 <- dat %>% group_by(Gene.Symbol) %>% mutate_each(funs(mean), -(0)) %>% distinct

head(dat2)
rownames(dat2) <- dat2$Gene.Symbol

MedulloSigs <- dat2
rm(dat)
rm(dat2)
```

# Now, let's subset this medullo data for the genes that are in the compound response signature. Then, we can assess differential discordance. 

```{r}
head(MedulloSigs)
```

```{r}
head(compound_sig)
cmpdGenes <- rownames(compound_sig)
  # obj.transpose <- t(obj@assays$SCT@scale.data) 
  cmpd_overlap <- rownames(MedulloSigs)[which(rownames(MedulloSigs) %in% cmpdGenes)]
  overlap <- MedulloSigs[cmpd_overlap,] # FileA
  overlap
  rownames(overlap) <- overlap$Gene.Symbol
  
  # overlap$Gene.Symbol <- NULL
  head(overlap)
  
  cmpd_ordered <- as.numeric(as.vector(t(compound_sig)))
  names(cmpd_ordered) <- rownames(compound_sig)
  cmpd_ordered
  cmpd_ordered2 <- cmpd_ordered[cmpd_overlap] # Character list in brackets orders to fit that character list...
  
  cmpd_ordered2
  
  print("Check that genes are all in the right order... ")
  head(rownames(overlap) == names(cmpd_ordered2))
  
  #
  head(rownames(overlap))
  head(names(cmpd_ordered2))
  
```

# Now set up each different tumor type as a vector or whatever to be able to calculate SC for each...  
  
```{r}

# SHH
head(overlap)
SHH <- overlap$Log2FC_SHH
names(SHH) <- rownames(overlap)  
  
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")
head(names(SHH) == names(cmpd_ordered2))

SC.SHH <- cor(cmpd_ordered2, SHH, method = "spearman")
  
# WNT
head(overlap)
WNT <- overlap$Log2FC_WNT
names(WNT) <- rownames(overlap)  
  
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")
head(names(WNT) == names(cmpd_ordered2))

SC.WNT <- cor(cmpd_ordered2, WNT, method = "spearman")

# G3
head(overlap)
G3 <- overlap$Log2FC_G3
names(G3) <- rownames(overlap)  
  
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")
head(names(G3) == names(cmpd_ordered2))

SC.G3 <- cor(cmpd_ordered2, G3, method = "spearman")

# G4
head(overlap)
G4 <- overlap$Log2FC_G4
names(G4) <- rownames(overlap)  
  
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")
head(names(G4) == names(cmpd_ordered2))

SC.G4 <- cor(cmpd_ordered2, G4, method = "spearman")

```

# So how do we make a figure showing that g3 is predicted over SHH, others?

First, can we subset to a signature that we can visualize by thresholding on fold change?

```{r}
G3

df <- as.data.frame(G3)
df

th <- subset(df, df$G3 > 0.1 | df$G3 < -0.1)

th

L1000_signature_data <- read.table(file = "matPH3_2_1_0.2_0.3_L1000_Batch2017_Regina_removed.txt", row.names = 1, header = TRUE)

head(L1000_signature_data)

target_compound <- "triptolide"

compound_sig <- as.data.frame(t(subset(L1000_signature_data, rownames(L1000_signature_data) == target_compound)))
compound_sig <- subset(compound_sig, rownames(compound_sig) %in% rownames(th))

data <- compound_sig$triptolide
names(data) <- rownames(compound_sig)
data

barplot(data, horiz = TRUE, col = "red")

pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)

pdf(file = "triptolide_subset_sig_heatmap.pdf")
pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)
dev.off()
```

# Now, can we just make a barplot of the spearman correlations?

```{r}
data <- as.numeric(c(SC.G3, SC.G4, SC.WNT, SC.SHH))
names(data) <- c("G3", "G4", "WNT", "SHH")
data

barplot(data, horiz = TRUE, col = "red")
pdf(file = "triptolide_spearmancorrelation_barplot.pdf")
barplot(data, horiz = TRUE, col = "red")
dev.off()
```

# Now, it would be pretty cool to cluster the data on this signature and see how it looks...

```{r}
library(dplyr)
MedulloSigs <- read.csv(file = "MedulloSigs.csv", skip = 1, header = TRUE)
head(MedulloSigs)

'%nin%' = Negate('%in%')
cols <- colnames(MedulloSigs)
cols
myvars <- subset(cols, cols %nin% c("Log2FC_G4", "Log2FC_G3", "Log2FC_WNT", "Log2FC_SHH", "MEDIAN_OVERALL", "MEDIAN_G4", "MEDIAN_G3", "MEDIAN_WNT", "MEDIAN_SHH", "X.1", "Probe.Set.ID", "X.2", "X.3", "X.4", "X.5", "X.6", "X.7", "X"))
dat <- MedulloSigs[myvars]
# head(dat)
# myvars2 <- c("Log2FC_G4", "Log2FC_G3", "Log2FC_WNT", "Log2FC_SHH")
# rownames(dat) <- dat$Gene.Symbol
dat <- subset(dat, dat$Gene.Symbol %in% colnames(L1000_signature_data))
head(dat)
```

```{r}
dat2 <- dat %>% group_by(Gene.Symbol) %>% mutate_each(funs(mean), -(0)) %>% distinct

head(dat2)
rownames(dat2) <- dat2$Gene.Symbol

# MedulloSigs <- dat2
# rm(dat)
# rm(dat2)

head(dat2)

names(cmpd_ordered)

dat3 <- subset(dat2, rownames(dat2) %in% rownames(compound_sig))

dat4<-dat3
dat4$Gene.Symbol <- NULL
rownames(dat4) <- dat3$Gene.Symbol

# rownames(dat3) <- dat3$Gene.Symbol
# dat3$Gene.Symbol <- NULL
pheatmap::pheatmap(dat4, scale = "row")

# How can we annotate this real quick. 

g <- as.data.frame(colnames(dat4))
g
for (i in 1:length(g$`colnames(dat4)`)){
  g$type[i] <- unlist(strsplit(as.character(g$`colnames(dat4)`[i]), split = ".", fixed = TRUE))[[1]]
}
g
e <- g
rownames(e) <- g$`colnames(dat4)`
e
e$`colnames(dat4)` <- NULL
pheatmap::pheatmap(dat4, scale = "row", annotation_col = e)

pdf(file = "triptolide_mb_clusteringHeatmap.pdf")
pheatmap::pheatmap(dat4, scale = "row", annotation_col = e)
dev.off()
```

